Toward sustainable irrigation practices safeguarding groundwater biodiversity and ecosystem services

Abstract

Groundwater provides much of the water used globally for irrigation and human consumption and is central to the One Health framework. Healthy groundwater depends on self-purification processes performed by diverse groundwater biota, but these processes can be threatened by the effects of irrigation. In the present article, we explore this threat using an interdisciplinary framework and propose recommendations for sustainable irrigation. We identified two major potentially harmful effects of irrigation on groundwater ecosystems: habitat loss from lowering water tables and irrigation-induced leaching of contaminants into groundwater. These effects can be mitigated by improving technological practices, crop selection, the use of natural small water retention measures, precision irrigation, and the controlled use of agrochemicals. The construction and operation of irrigation systems should consider hydrogeological conditions. We recommend prioritizing groundwater biomonitoring at abstraction and irrigation sites, considering different aquifer types, and implementing advanced methods to identify multiple contamination sources.

Groundwater ecosystems contain most of the unfrozen freshwater on Earth and are widespread across all continents (Alley 2009, Reinecke 2022). They provide essential ecosystem services that include the provision of clean water for drinking and irrigation (Griebler et al. 2014, Griebler and Avramov 2015, 2019). Moreover, groundwater has been proposed to be a key ecosystem that functionally links all aquatic ecosystems and is vital for the maintenance of their health (Zhou et al. 2014, Robertson et al. 2023, Saccò et al. 2024). Therefore, groundwater plays a crucial role in human well-being and global ecosystem health and should be considered as one the pillars of the concept of One Health, an integrated approach that recognizes that the health of humans, plants, animals, and ecosystems is interconnected and functionally linked (World Health Organization 2022). Despite its importance, groundwater is one of the most threatened ecosystems in the world because of climate change and land use and land management changes (Ripple et al. 2017). All anthropogenic activities on the surface, such as hydrotechnical constructions, industrial and agricultural activities, waste management, and contaminant spills, eventually reach groundwater, accumulate in it, and reappear in surface waters again (Di Lorenzo et al. 2012, Kath et al. 2018). The loss of groundwater ecosystem services would have global and profound negative consequences for human and ecological health. The protection and sustainable management of groundwater is therefore imperative (Mammola et al. 2019, Wynne et al. 2021, Niazi et al. 2024).

Legal instruments dedicated to the protection of groundwater vary from place to place and emphasize different measures to be protected while consistently neglecting groundwater biota (Griebler et al. 2023). An illustrative case is the European Union, where groundwater is protected by the Groundwater Directive (2006/118/EC), which explicitly called for research on groundwater ecosystems to secure their extent and quality and to protect the viability of aquatic and terrestrial groundwater-dependent ecosystems (Di Lorenzo et al. 2024). Indeed, groundwater is a true ecosystem, harboring specialized biota that are adapted to survive in this permanently dark, oligotrophic environment (Hüppop 2000, Christiansen 2005, Fillinger et al. 2023). We use the term groundwater biota for microbial and eumetazoan organisms primarily living in groundwater (in contrast to occasional or accidental residents; Sket 2008). These species include narrow endemics, sometimes occupying only a few square kilometers (Trontelj et al. 2009, Bregović et al. 2019, Borko et al. 2023) and relict lineages that survived surface extinctions by sheltering in groundwater (Humphreys 2000, Borko et al. 2021, Cooper et al. 2023). These animals represent a substantial fraction of the continental freshwater diversity in Europe (Stoch and Galassi 2010) and on the globe (Marmonier et al. 2023). However, presently, groundwater monitoring quantifies only the quantitative, physicochemical, and hygienic status of aquifers, and proposed changes to the EU directive continue to overlook the importance of groundwater biota to water quality, human and ecosystem health, and biodiversity goals (European Commission 2022, Di Lorenzo et al. 2024). Similar problems exist in the United States, where the rules for protection of groundwater systems are focused largely on drinking water protection, with no explicit consideration given to groundwater biota and ecosystems or to the roles they play in maintaining groundwater quality (EPA 2006).

Groundwater biota provide essential ecosystem functions, such as nutrient cycling and a carbon sink (Fillinger et al. 2023, Mermillod-Blondin et al. 2023), that are critical to the self-purification processes in aquifers and are therefore directly linked to the provisioning of clean drinking water and global human health (Griebler et al. 2014, Griebler and Avramov 2015, Saccò et al. 2024). However, the exploitation of groundwater for different purposes may lead to colliding interests, because the quantity and quality of the water needed may be very different for drinking water, irrigation in agriculture, and industrial uses. Probably, from a human perspective, the most important service of groundwater ecosystems is the provision of drinking water, which heavily relies on the high-quality water only provided by healthy and functional groundwater ecosystems (Hose et al. 2023). Drinking water production and the conservation of groundwater biodiversity are not necessarily in conflict, because both require the protection of land and water. However, under the central tenet that groundwater biota are essential for self-purification processes (Fillinger et al. 2023, Hose et al. 2023, Mermillod-Blondin et al. 2023), we question how the exploitation of groundwater for different purposes affects groundwater ecosystem health. Specifically, we explore the effects of water abstraction and the application of that water to agricultural fields for irrigation on groundwater biodiversity and the provision of essential ecosystem services.

Water use has been increasing globally by 1% per year over the last 40 years and is expected to grow at a similar rate until 2050 (UNESCO 2023). Groundwater provides half of the water used for domestic purposes (UNESCO 2023) and supplies over 40% of global irrigation demand (Kuang et al. 2024). Although only 20% of all agricultural land is irrigated, it accounts for 70% of all water abstracted for human use (Brauman et al. 2016). Half of the global expansion of irrigated agriculture in the twenty-first century has been in water-stressed regions, putting a considerable burden on groundwater bodies (Mehta et al. 2024). In Europe, the construction of irrigation systems began increasing in the 1960s, including on the best agricultural land. This construction peaked in 1990s and subsequently slowed down as the low food prices no longer economically justified its expansion into suboptimal areas (Rosa et al. 2019). In roughly the same period, alerts of inadequate and suboptimal irrigation systems emerged (Rosa et al. 2019). On a global scale, 85% of all irrigation is flood irrigation. Water is conveyed via open canals and is applied to the fields with an overflow. This technique typically results in substantial loss of water, where, at times, only 30% of the water eventually reaches the plants (Puy et al. 2022).

The application of sustainable irrigation is in its infancy. In this article, we adopt the European Irrigation Association’s definition of sustainable irrigation, which is “an ensemble of fair technologies and practices for the increasingly optimized use of water, energy, fertilizers, and other resources for irrigated agriculture, landscape, and ornamentals so that the natural resources are equitably used for the welfare needs of the present and future generations.”

Ineffective irrigation in combination with an excessive use of fertilizers can worsen groundwater quality (Fan et al. 2014) and can have direct and indirect effects on surface ecosystems. Irrigation can directly benefit some hygrophilous organisms (Romano et al. 2014, Schirmel et al. 2014, Gerlach et al. 2023) and can negatively affect others (Peterson and Cooper 1987, Fagúndez et al. 2016). Negative indirect impacts of irrigation on biota are typically a consequence of agricultural intensification—for example, through higher input of fertilizers and pesticides (Graf et al. 2014, 2016a, Müller et al. 2016b) and increased water use, resulting in soil salinization (Dougherty et al. 1995), a drop of groundwater and surface water levels due to overabstraction (Jasechko et al. 2024), and degradation of the ecosystems (Green et al. 2024). Changes to the groundwater biota linked to irrigation have been shown in isolated studies (Di Lorenzo and Galassi 2013, Korbel et al. 2013b, 2022, Marmonier et al. 2018), but there has not been a systematic exploration of the mechanism of changes and the broader impacts of irrigation on groundwaters and the delivery of ecosystem services (Dumas 2004, Englisch et al. 2024).

In this Viewpoint, we argue that sustainable groundwater management strategies should be developed and promoted within the One Health framework and that it should align the protection of groundwater biota to secure healthy drinking water with sustainable irrigation to secure healthy food supply. To make progress toward sustainable groundwater management, we first assess how irrigation may affect the quality and quantity of groundwater and how sensitive groundwater biota are to these changes. To provide a clear overview, we summarize the key threats of irrigation on groundwater quality, quantity, and biota in table 1. Because there are virtually no focal studies, we open a broad perspective and review studies in hydrogeology, agriculture, community ecology, and ecotoxicology and integrate them into a theoretical framework that can serve to guide future basic and applied research. We then confront these results with different irrigation technologies to provide guidelines for sustainable irrigation, which is beneficial for agricultural production, drinking water provision, and the protection of the biodiversity in groundwater ecosystems. Finally, we provide best-informed recommendations on how the effects of water abstraction on groundwater fauna may be better addressed, which can be used in irrigation-related decisions.

Table 1.

An overview of threats to groundwater and its fauna associated by irrigation.

Threat	Source	Impact
Lowering of the water table	Direct groundwater abstraction exceeding natural recharge rates	Leads to aquifer depletion, reduced habitat availability, and weakened connection with surface ecosystems.
Weakened connectivity with surface water	Abstraction of water from rivers or lakes reducing hydraulic gradients	Impairs exchange with surface water, leading to changes in groundwater habitats.
Enhanced infiltration of surface water	Systematic overabstraction of groundwater close to surface water bodies, reversing groundwater–surface water interactions	Decreases in or complete loss of baseflows, modification of groundwater properties.
Increased recharge from surface irrigation	Excessive irrigation replenishment	Alters groundwater levels, and possibly groundwater quality.
Impact of reservoir construction	Damming of rivers to create irrigation reservoirs	Colmation reduces permeability, alters groundwater recharge, and impacts biota in adjacent habitats.
Enhanced transport of soil contaminants	Excessive irrigation leading to leaching of fertilizers and pesticides	Increased infiltration of agrochemicals into groundwater, causing toxicity to groundwater organisms and eutrophication.
Microbial contamination	Use of contaminated water or manure in irrigation	Introduction of pathogens and alteration of microbial community structure in aquifers.
Trace organic microcontaminants	Use of reclaimed or recycled wastewater for irrigation	Presence of endocrine disruptors, pharmaceuticals, and personal care products in groundwater, with unknown long-term ecological effects.
Microplastic pollution	Degradation of plastic irrigation systems and contaminated irrigation water, transport from contaminated soils	Accumulation of microplastics in aquifers, ingestion by groundwater biota, and potential trophic transfer of contaminants.
Altered biogeochemical processes	Enhanced leaching of contaminants and altered environmental conditions	Disruption of self-purification processes and denitrification, affecting groundwater quality and ecosystem functions.

The effects of irrigation on the properties of groundwater habitats

We use the term groundwater in a broad sense at the landscape scale, referring to water in unconsolidated sediments at all depths, as well as water in consolidated sediments of fractured and karstic rock (Culver and Pipan 2014, 2019, Robertson et al. 2023). The management of groundwater should consider hydrogeological properties of the groundwater body. In general, groundwater flow and transport processes can be determined on the basis of aquifer characteristics (Hartmann 2022).

Porosity in intergranular aquifers is a consequence of contact between grains in the sediment or rock (Brenčič et al. 2009). The groundwater velocity in this type of aquifer is relatively homogenous, and the groundwater flow and levels are responsive to meteorological conditions albeit with some delay. The risk of pollution of the aquifer decreases with distance from the source of pollution.

In karst systems, water bodies are connected to each other through a complex network of channels at various levels of the carbonate massif, in which system connectivity and flow are dependent on the water level (Ravbar 2013). Channel porosity dominates; water velocity in the channels is much higher than in the other parts of the aquifer rock (Brenčič et al. 2009), meaning that the distribution of groundwater flow velocity in the aquifer is very heterogeneous. As a result, the risk of pollution from the source does not depend on its proximity, and pollution can spread very quickly over long distances. The retention and filtering properties of this type of aquifer are low. The conditions in the aquifer are highly dependent on meteorological conditions. Turbidity of the water is common (Brenčič et al. 2009). The underground connections do not necessarily follow topographical catchment boundaries, which is often reflected in the distributions of groundwater species (Konec et al. 2016, Delić et al. 2021).

In fissured aquifers, the porosity of the fissures and joints is predominant, but intergranular porosity and channel porosity may also be present (Brenčič et al. 2009), and groundwater flow can be laminar or turbulent. Depending on the flow characteristics, this type of aquifer can be similar to intergranular or karstic aquifers (Hartmann 2022).

The unsaturated zone above the groundwater table is of great importance in providing water and nutrients crucial to the biosphere (Stumpp and Kammerer 2022). The movement of water and the transport of solutes in the unsaturated zone are key processes that influence both the quantity and quality of groundwater (Koroša et al. 2020). Unsaturated zone processes are therefore very important for the quantity and quality of groundwater available to ecosystems. In addition to dispersive flow, preferential flow can occur in the unsaturated zone (Nimmo 2005). Preferential flow paths have a higher vertical flow velocity (short transit time), which can quickly transport contaminants into groundwater, wheras dispersive flow is characterized by large volumes of water that are transported relatively slowly through the unsaturated zone (Koroša et al. 2020).

The effects of water abstraction and irrigation on water quantity

Water displacement through abstraction and irrigation naturally leads to a local decrease or increase in water volume, respectively. Rapidly declining groundwater levels (greater than 0.5 meters per year) are common in intensive agricultural regions where over one-fifth of the land is cultivated. In contrast, rapidly declining groundwater levels are almost nonexistent in areas where less than 1% of the land surface is cultivated (Jasechko et al. 2024). The effects of water abstraction on habitat characteristics can vary greatly depending on the location and type of abstraction. We focus in the present article on the effects of water abstraction in nonkarst regions that have been better studied. We identified four impacts in nonkarst regions and one indirect impact related to reservoir construction (table 1).

Direct abstraction of groundwater lowers the water table (Hancock 2002) or the piezometric surface in confined aquifers and can lead to aquifer depletion (Benaafi et al. 2022) when the rate of abstraction exceeds the rate of natural recharge. A decrease in the level of groundwater has several potentially negative impacts: a weaker connection between the surface water and the groundwater, reduced or a complete loss of flow in streams and springs that maintain the connection between the surface and groundwater habitats, and a loss of habitat availability (Uhl et al. 2022). Weaker exchange with the surface water may affect the groundwater supply with food and oxygen (Malard and Hervant 1999) that can result in multiple, site-specific outcomes, including those with a highly negative impact on groundwater biota (e.g., hypoxia or pronounced oligotrophy). It is noteworthy that, in specific cases of highly polluted surface water, a weaker exchange with the surface water may lower the risk of pollution. Experimental observations indicate that at least some groundwater species can follow the lowering groundwater table. However, some groundwater biota may remain trapped in wet pockets and may die out after desiccation (Stumpp and Hose 2013).

Water withdrawal from surface waters, such as rivers or lakes, may lower the water level and hydraulic gradients that drive surface water into hyporheic and underlying phreatic zones and may lead to a weakened exchange between the surface and subterranean water (Hancock 2002). The potential negative impacts of the weakened connectivity may include decreased oxygen concentrations, lower infiltration of organic matter, and less favorable conditions for life.

Groundwater abstraction close to surface water bodies may enhance the infiltration of surface water (Hancock 2002, Gleeson and Richter 2018, Gleeson et al. 2020). Furthermore, systematic overabstraction can reverse historical groundwater–surface water interactions near surface water bodies, with decreases in or a complete loss of baseflows (Uhl et al. 2022). The connections increasingly move only from the surface water to the groundwater systems. This increases the frequency and magnitude of nutrients and contaminants entering the groundwater systems in regions where groundwater once discharged to surface environments (de Graaf et al. 2019, Scanlon et al. 2021). In the case of riverine pollution, enhanced infiltration potentially increases the movement of pollutants into groundwater, leading to degraded quality of the hyporheic zone and lowering its biofiltering capacities (Mauclaire and Gibert 1998). Enhanced recharge rates from surface to groundwater may potentially lead to differences in groundwater quality and could be—at least in theory—as important as changes caused by the infiltration of irrigation water described in the next section.

Excessive irrigation (e.g., through surface irrigation) can replenish the groundwater volume beneath irrigated areas. In shallow aquifers, irrigation can contribute up to 30% of the recharged water (Qi et al. 2023), and the recharge can be faster than by natural means (Kurtzman and Scanlon 2011).

Finally, damming rivers to create water reserves for irrigation can have indirect but profound effects on a river system and the underlying hyporheic zone and groundwater. Dams slow down the water flow, leading to the accumulation of fine sediments and colmation in the water storage area (Brunke 1999, Zagmajster et al. 2024) and, as a consequence, may restrict the exchange of river and hyporheic water (Schmutz and Moog 2018). A lowered oxygen level because of colmation reduces species richness (Descloux et al. 2013, Zagmajster et al. 2024) and modifies the species composition of communities (Descloux et al. 2014, Zagmajster et al. 2024). Dams also increase hydraulic heads and gradients around the water storage area, which could enlarge available groundwater habitats. However, depending on the local conditions, large amounts of reservoir water can be forced into groundwater systems, which alters the groundwater properties and quality (Ammar et al. 2015) and likely affects the biological communities in adjacent groundwater habitats.

The effects of irrigation on water quality

Irrigation can affect groundwater quality in different ways (table 1). Excessive irrigation may change the environmental fate of soil contaminants, such as fertilizers and other agrochemicals. Most studies have demonstrated enhanced transport of pesticides from the upper soil layers to groundwater after irrigation (Müller et al. 2007). Such transport is particularly pronounced in flood irrigation (Fan et al. 2014), which can increase the inputs of nitrogen-based chemicals and agrochemicals to groundwater by up to 50% (Qi et al. 2023). Irrigation, when using contaminated water or in combination with the application of manure, may also enhance the microbial contamination of aquifers (Krauss and Griebler 2011, Frey et al. 2015, Li et al. 2015, Weaver et al. 2016).

The use of contaminated, recycled, or reclaimed wastewater for irrigation is another avenue for the contamination of groundwater (Malakar et al. 2019, Benaafi et al. 2024). For example, reclaimed wastewater may contain trace amounts of organic microcontaminants that are not removed during treatment (e.g., endocrine disruptors, plasticizers, pharmaceuticals, and personal care products; Helmecke et al. 2020). The use of industrial wastewater for irrigation has been reported as a source of heavy metal pollution to groundwater (Al-Huqail et al. 2022). Besides conventional contaminants, novel contaminants such as microplastics have been identified in irrigation water in large amounts (Zhou et al. 2020). Furthermore, plastic irrigation systems, including pipes and sprinklers, themselves present a contamination source, because these commonly end up as mismanaged waste, which eventually degrades in the environment to microplastics (Huerta Lwanga et al. 2022, Liao et al. 2023). There is growing empirical evidence of the presence of microplastics in groundwater, including in karst caves (both touristic and nontouristic), in aquifers in unconsolidated sediments, and in hyporheic zones (Balestra et al. 2023, Sforzi et al. 2024, Zhang et al. 2024). Microplastics can be ingested by groundwater biota and were found to account for up to 1% of the gut volume in some groundwater isopods (Sforzi et al. 2024).

The consequences of the enhanced leaching of contaminants to groundwater are not well understood (Koroša et al. 2020, Fillinger et al. 2023, Groote-Woortmann et al. 2024). In groundwater ecosystems, self-purification processes, including the degradation of organic pollutants and denitrification, rely not only on the presence of specific microorganisms doing the job but on environmental conditions that allow individual processes to occur. Although nitrate is reduced efficiently only in the absence of oxygen and in the presence of a suitable electron donor (e.g., organic matter, sulfide), some organic contaminants are preferentially degraded under oxic or anoxic conditions (Meckenstock et al. 2015). Moreover, biotransformation of contaminants is often a matter of concentration, which sometimes makes the removal of trace contaminants energetically impossible for microbes (Kundu et al. 2019, Sun et al. 2021). Biogeochemical processes in groundwater are intertwined among different functional groups of microorganisms and regularly depend on syntrophic collaboration (Wrighton et al. 2014, Anantharaman et al. 2016). The effectiveness of the processes therefore depends on the presence of all groups. Although it has been shown that microbes can degrade a broad array of contaminants, most of the underlying processes are understudied in groundwater, and further research is needed (Fillinger et al. 2023). Similarly, it is not clear how contaminants spread through groundwater trophic networks. The effects of novel contaminants are the subject of ongoing research (Gong et al. 2023, Liu et al. 2023).

The impacts of irrigation on groundwater quality are likely related to the distance between the soil surface and the groundwater. As irrigation water drains downward through the vadose zone it interacts with, soil, microorganisms, organic matter, and minerals, it gains and loses nutrients and oxygen (Brunke et al. 1997, Shen et al. 2015). In unconsolidated sand and gravel aquifers in the United States and France, dissolved organic carbon concentration in groundwater decreased with increasing vadose zone depth (Pabich et al. 2001, Datry et al. 2005). Just as dissolved organic carbon concentrations vary with groundwater depth, it is likely that the agrochemicals and nutrients, such as pesticides and nitrates, associated with irrigation are also metabolized or retained in the unsaturated zone, leading to lower concentrations of those compounds in deeper aquifers.

Sensitivity of groundwater communities to environmental change

Subterranean organisms have evolved and adapted to the stable and oligotrophic groundwater environment over thousands of years and, as a result, are inherently vulnerable to environmental change. Their life cycles are long, and the organisms are limited in dispersal; therefore, the recovery times of disturbed communities are presumably long (Hose et al. 2022, Lunghi and Bilandžija 2022). Communities rely on detritus and microbial biomass (Francois et al. 2016, Mermillod-Blondin et al. 2023) and are generally functionally truncated (Gibert and Deharveng 2002), although they, on some occasions, include up to four trophic levels (Hutchins et al. 2014, 2016, Premate et al. 2021). The links among organic carbon (including contaminants), bacterial productivity, and metazoan groundwater communities are poorly understood (Griebler et al. 2022). In this section, we review correlative ecological studies, as well as ecotoxicological and experimental studies that address problems such as those that may emerge with irrigation.

Response to a drop of groundwater table

Irrigation practices affect some groups of groundwater organisms, leading ultimately to their local extinction and replacement with surface faunas (Dumas 2004). The abstraction of water for irrigation, particularly from deep karst aquifers, has been linked to declines in the abundance of groundwater fauna (Buzek 2023, Weber 2023). With a decline in the groundwater table, individual organisms become trapped in the unsaturated zone and eventually die unless the water recharges. To mitigate drought-related mortality, the species either migrate downward or resist the drought. The effects of a drop in the groundwater table depend on the type of aquifer, the speed of groundwater table decline, and species autecology (Stumpp and Hose 2013).

Groundwater species may show a distinct vertical distribution (Hose et al. 2017). Species that aggregate in the upper layers, close to the water table and overlying the unsaturated zone, are expected to be more sensitive to water table declines than species with more even vertical distribution (Stumpp and Hose 2013). However, even species aggregated in the upper zones of groundwater may respond differently to a declining water table. For example, both copepod and bathynellacean crustaceans often live near the surface. After experimentally induced drought, 25% of bathynellacean and 88% of copepod crustaceans remained entrapped in the unsaturated zone of the unconsolidated sediment, suggesting that drought affects different taxa very differently (Stumpp and Hose 2013). We hypothesize that water abstraction for human uses exacerbates the effects of irregularly occurring droughts. However, the effects of drought and water abstraction are additive.

The vertical migration of fauna also depends on the structure, heterogeneity, and pore sizes of the sediment and the size of the animal (Mathers et al. 2014, Patel et al. 2021). Pore size, determined by the size and shape of sediment particles, can act as a physical barrier constraining species’ migration, depending on the relative sizes of the species and the average pore sizes. In general, small animals such as copepods and bathynellaceans prefer fine to coarse sands, whereas larger amphipods prefer coarser sediments (Korbel et al. 2019). Only minute interstitial species and annelid worms are likely to pass through silt (Korbel et al. 2019).

A different and possibly complementary strategy to vertical migration is resistance to drought. Many species can survive the drought by burrowing into moist sediments (Gilbert et al. 2018). However, experimental data show that resistance to drought differs among groups. Bathynellaceans, for example, survive 48 hours in substrate with 6% saturation of water, whereas copepods’ survival of the same period requires 16%–33% habitat saturation (Stumpp and Hose 2013).

The effects of the drought may also be indirect, regulated by bottom-up mechanisms associated with the changes of microbial biomass in biofilms. Evidence suggests that fluctuating water levels at least temporarily affect microbial activity (Weaver et al. 2016) and likely influence the survival of immobile microbial biofilms (but see Coulson et al. 2021). Whereas the structure of metazoan communities is most strongly correlated with habitat properties, microbial communities are more strongly correlated with water quality and seasonal variations in water levels. It seems reasonable to assume that fluctuations in water level affect microbial biofilm more than metazoan taxa and select for microbes that are resistant to those fluctuations (Korbel et al. 2013b, Korbel and Hose 2015). The loss of biofilm, an important source of food in groundwater communities, may have long-term and profound effects on species diversity and abundance. Indeed, studies from Italy showed that a short-term drop of the groundwater table decreased the abundance of individual species (Di Lorenzo and Galassi 2013).

Overall, groundwater communities may respond to fluctuations of the water level in either direction, depending on a combination of environmental factors. Noteworthy are the observations from Australia, where aquifers replenished by irrigation water showed greater species richness than nonirrigated sites (Korbel et al. 2013a). Although the causal mechanism for increased richness was not elucidated, this result shows the importance of groundwater volume (and higher nutrient loadings, in this case) in supporting species richness and abundances. The amount of recharge to an underlying aquifer, however, depends on the nature of the agricultural activity. The type of agricultural activity also influences the groundwater quality (as was discussed above), and the potential consequences of water quality deterioration are discussed in the next subsection.

Box 1.

Further impacts of irrigation practices on groundwater communities.

Alongside contamination from inorganic nitrogen species and pesticides, coastal aquifers face multiple threats including saltwater intrusion due to the excessive extraction of groundwater for crop irrigation. Such salinization endangers specialized groundwater species, notably groundwater copepods and syncarids, which are sensitive to sodium chloride, with harmful concentrations ranging from 2.84 to 7.35 grams of sodium chloride per liter. These detrimental effects intensify under higher temperatures (Castaño-Sánchez et al. 2020b).

In addition, there is growing concern regarding the potential infiltration of surface-dwelling species into subterranean ecosystems triggered when irrigation practices increase the availability of organic matter that can sustain surface invaders, which may struggle to survive under the typically oligotrophic conditions. This migration could alter established trophic dynamics, as surface water species, characterized by their higher metabolic activity and fecundity, may outcompete their groundwater counterparts. The abundance of surface water taxa is frequently seen as a sign of deteriorating groundwater quality due to agricultural activities (Korbel and Hose 2017, Di Lorenzo et al. 2020).

Irrigation methods can influence the transport of pathogens from animal feces into groundwater, affecting the indigenous microbial community. A study in New Zealand demonstrated that Escherischia coli had higher persistence and thrived better under sprinkler irrigation conditions compared to flood irrigation. Conversely, other pathogens, such as Campylobacter, did not show significant differences in transport between the irrigation methods, primarily because of their poor survival rates (Weaver et al. 2016). In a similar vein, irrigation might enhance the transport of surface and soil originating microbes into groundwater. To our knowledge, this issue has not been studied in detail.

Groundwater heat pumps are increasingly implemented in intensive livestock farms, merging seamlessly with irrigation systems (Alberti et al. 2018). These systems involve reinjecting warmed groundwater upstream during colder seasons and utilizing it for irrigation in warmer periods. This dual-use system not only ensures efficient climate control within stables but also promotes the recycling of nitrogen within agricultural fields. Nevertheless, this practice can induce significant variations in groundwater temperature, potentially harming sensitive groundwater fauna. Recent research highlights that obligate groundwater species have narrow thermal niches and have limited adaptability to temperature fluctuations during both short-term (Di Lorenzo and Reboleira 2022) and long-term acclimation (Di Lorenzo et al. 2023). Groundwater warming affects their survival and behavioral patterns, and impairs the ecosystem services they provide (Brielmann et al. 2009, Griebler et al. 2016, Vaccarelli et al. 2023).

Finally, water abstraction can lead to direct removal of animals, as is the case with Texas subterranean catfish (Buzek 2023).

Sensitivity of groundwater organisms to selected agricultural pollutants

Ecotoxicological studies using groundwater organisms are challenging to conduct and rarely realized (Di Lorenzo et al. 2019). In general, groundwater species may differ in response to pollutants from surface species. However, the response of groundwater species to pollutants varies (Di Marzio et al. 2009, Jemec Kokalj et al. 2022). We limit our review to studies of the potential toxicity of nitrogen-based substances and pesticides, because these are two commonly investigated groups of agricultural contaminants in groundwater ecotoxicological studies (Groote-Woortmann et al. 2024). Additional and less explored impacts of irrigation practices on groundwater communities are presented in box 1.

The only European subterranean amphibian, the olm (Proteus anguinus), is potentially very sensitive to nitrate. Kolar (2018) estimated the nitrate threshold value for the olm on the basis of observed concentrations calculated from other amphibian data. This value is five times lower (9.2 milligrams [mg] of nitrate per liter [L]) than the nitrate directive threshold value (50 mg nitrate per L; Kolar 2018). Arthropods, on the other hand, are less sensitive, and their effect values were commonly found at concentrations higher than the nitrate directive threshold value (50 mg nitrate per L). One of the few recent studies on groundwater crustaceans compared nitrate toxicity between surface species (Gammarus fossarum) and groundwater species (Niphargopsis casparyi, Proasellus slavus; Gerhardt 2020). The effects were most pronounced for N. casparyi, which showed signs of decreased locomotion at 50 mg per L and decreased survival at 100 mg per L after acute (24 hours) exposure. After chronic exposure (5 weeks), the effects were observed for all three species at 50 and 100 mg per L, with G. fossarum being the most sensitive. As Di Lorenzo and colleagues (2021) concluded in their review of some earlier work on stygobiotic crustaceans (copepods), nitrate was acutely lethal at concentrations significantly higher than the 50 mg per L nitrate directive threshold value. Accordingly, the composition and dynamics of the cyclopoid assemblage in the Ariège alluvial aquifer (in the French Pyrenees) were not affected by the high levels of nitrate pollution resulting from nutrient leaching and irrigation practices (Dumas et al. 2001). The analysis of 25 wells in a highly nitrate polluted area showed a decline in copepod species’ abundances but not in species richness (Di Lorenzo et al. 2021). However, there are indications that long-term exposure to high concentrations of nitrate leads to structural changes of populations of groundwater species similar to that shown for freshwater crustaceans (Hickey 2013). Noteworthy was the observation of fewer young animals in nitrate polluted wells, suggesting either the negative effects on individual fertility or larval survival (Di Lorenzo et al. 2021). Ammonium is more toxic than nitrate, although it never reaches the concentrations of nitrates. Moreover, groundwater copepod species seem to be more sensitive to ammonium than are their surface relatives (Di Lorenzo et al. 2015, Di Marzio et al. 2018, 2021).

Nitrate pollution due to irrigation and fertilizer use has been linked to changes in groundwater microbial communities (Korbel et al. 2022). Although nitrate concentrations were not always greater at irrigated than at nonirrigated sites, the relative abundances of nitrifying bacteria (such as Nitrospumilalles and Nitrosphaerales) were overall greater than those of denitrifying bacteria at irrigated sites, whereas the abundances of nitrifying and denitrifying bacteria (e.g., Bacillales and Pseudomonadales) were similar at nonirrigated sites (Korbel et al. 2022). Nitrifying bacteria oxidize ammonium to nitrate, and an increase in their abundance may be an indicator of ammonium pollution; that is, the ratio of nitrifying to denitrifying bacteria may serve as a bioindicator of irrigation impact on groundwater microbial communities (Korbel et al. 2022).

Pesticides are among the most studied contaminants in ecotoxicological studies of groundwater fauna and other aquatic organisms (Groote-Woortmann et al. 2024), although there have been far fewer studies than for surface freshwater environments. Altogether, 19 different pesticides have been tested in eight studies (Groote-Woortmann et al. 2024). In terms of acute exposure, the insecticide Fenpropathrin emerges as the most toxic pesticide to groundwater metazoans, affecting the survival of groundwater copepods at concentrations as low as 6 nanograms per L. In general, insecticides pose the most severe threat, followed by fungicides and herbicides. Fungicides manifest toxicity at concentrations measured in micrograms per liter, whereas herbicides demonstrate toxicity at concentrations exceeding 1 grams per L. Groundwater species seem may be more sensitive to agrochemicals than surface water taxa are (e.g., Hose 2005, Di Lorenzo et al. 2014). This suggests that the current groundwater quality guidelines, which are based on the sensitivity of surface water species, may not adequately protect groundwater ecosystems (Hose 2005, Di Lorenzo et al. 2018).

With the absence of photosynthetic organisms in groundwaters, it is unlikely that herbicides that target plant photosystems would directly affect groundwater ecosystems, whereas pesticides that target arthropods and fungi may have greater direct effects because of the dominance of these groups in groundwater habitats (Hose 2005). However, the synergistic interactions among common herbicides, such as atrazine and organophosphate pesticides (e.g., Choung et al. 2011), highlights the importance to consider the toxicity of mixture of chemicals for groundwater fauna, which have, to date, been rarely investigated (Castaño-Sánchez et al. 2020a, Groote-Woortmann et al. 2024). The use of nanopesticides provides an emerging challenge. Pesticides adsorbed by or encapsulated in nanoparticles can have different properties from the original pesticide (e.g., Grillo et al. 2012), particularly in terms of persistence and solubility (and therefore mobility), which may require a rethinking of the processes of contamination and the fate of contaminants in groundwaters below land subject to irrigation.

Advancing agricultural resilience and sustainability: From natural small water retention measures to precision irrigation

Irrigation and water retention in agriculture have been developing in two directions. The first direction aims to reduce the need for irrigation and fertilization. Natural small water retention measures (NSWRMs) increase water retention, reduce soil erosion vulnerability, improve agrobiodiversity for higher resilience of ecosystems to changes, and improve water quality (Curk and Glavan 2023, Magnier et al. 2024). NSWRMs include measures such as terracing (Deng et al. 2021), strip cropping along contours, controlled traffic farming, conservation farming, low till to no till agriculture (Gozubuyuk et al. 2015), crop rotation (Wang et al. 2023), green cover and intercropping, mixed cropping, the use of green mulch, crop and variety selection, maintaining permanent grassland especially along streams and at flood plains, reduced stocking density, and appropriate herding (European Commission 2015). In addition, riparian buffer strips, hedgerows, and green wind breaks are an effective way to reduce nutrient transport, improve water quality, and reduce evapotranspiration (Nsenga Kumwimba et al. 2024). Furthermore, hydromorphological measures such as basins and ponds (Uusheimo et al. 2020), wetland restoration and management, remeandering, and establishing slow infiltration of surface water to groundwater are measures that, in combination with others, will improve the water availability in agricultural landscapes (Iglesias and Garrote 2015). The efficiency and relative costs and benefits of individual NSWRMs is systematically documented through World Overview of Conservation Approaches and Technologies, which promotes the reporting, sharing, and use of knowledge to support adaptation, innovation, and decision-making in implementation measures. The above-listed NSWRMs are partially supported by agricultural policies in some countries. At the EU level, NSWRMs are promoted to some extent by water policies (European Commission 2014, 2015) but particularly by the new EU Common Agricultural Policy. Many of these measures are either supported through the strengthened mechanism of conditionality, meaning they are mandatory for those participating in the Common Agricultural Policy (i.e., greening buffer strips), or are financed as voluntary measures under the direct payments of the climate, environment, and animal welfare scheme. Nevertheless, Europe-wide research shows that a transition to increased implementation of NSWRMs requires further efforts, especially in the form of improved technical, financial, administrative, and training support for farmers and better harmonization of water and agricultural policies to improve coherence at the national and local levels (Cvejić et al. 2023). The use of an evidence-base strategy for targeted implementation (i.e., the optimal scale for measurable change) is still largely missing (Zhao et al. 2024).

The second direction of the development of irrigation practices has been maximizing the efficient use of water for irrigation. Systematic replacement of open channel and gravity systems with pressurized irrigation systems, incentivized (and obligatory) installation of irrigation and flow meters, systems for the regular maintenance of irrigation systems, and incentives for the purchase and installation of soil-water monitoring equipment are believed to contribute to improved practices to safeguard groundwater from overuse. At the user end, precision irrigation (i.e., irrigation that provides to every plant a sufficient but not excessive volume of water; Anjum et al. 2023) and improved irrigation scheduling based on plant water demand can reduce groundwater use more than 40% and thereby significantly reduce groundwater level decline (Feng et al. 2024). Zhang and colleagues (2024) indicated that reducing the area of surface irrigation and instead using sprinklers with higher irrigation efficiency protects groundwater bodies from overexploitation (Zhang et al. 2024). These irrigation practices need to be combined with other measures, such as regionally limiting certain crops and adjusting crop and variety selection (Paswan et al. 2024).

In addition to increasing water use efficiency, the reduction of nitrogen input from fertilizers to soils is suggested as a baseline measure to manage diffuse agricultural pollution of groundwater. Landscape hydromorphological measures, along with vegetation (forests, permanent grassland), is needed to supplement groundwater recharge with the beneficial dilution effect on dissolved nitrate (Rotiroti et al. 2023).

Recommendations for sustainable irrigation

There are two major and potentially detrimental effects of irrigation on groundwater biota and ecosystem services: the lowering of the water table associated with water abstraction and the potentially increased leakage of contaminants into groundwater at the site of irrigation. It is important to note that these two effects may be spatially separated, so that a reduction in the water table can occur around the point of water abstraction, whereas a deterioration in water quality is expected under the irrigated areas. Therefore, when studying the impact of irrigation on groundwater and its biota, the areas of water source and recharge should be considered. The effects of irrigation on groundwater fauna have not been practically studied. Although we know that groundwater ecosystems under irrigated land often have poorer health (Korbel and Hose 2017) but often more abundant fauna (Korbel et al. 2013), the exact mechanisms for these changes are unclear, and our ability to predict the likely changes in groundwater ecosystems due to irrigation is limited. This is a critical and urgent concern, because the land area under irrigation is projected to increase annually by 1% over the next half century because of climate change (UNESCO 2023), in parallel with increasing demand for water for irrigation and other uses. Our scientific knowledge of the impacts of irrigation and of the needs of sustainable groundwater management is not keeping pace with groundwater demand and exploitation. We therefore focus on the key knowledge gaps that should be addressed as a priority but also consider what should be the best practice for a transition to sustainable groundwater management. To mitigate the negative impacts of irrigation on groundwater biota and groundwater itself, we need a combination of biodiversity and soil conservation measures, technology development, and social incentives that promote more efficient irrigation practices (figure 1). Below, we present recommendations to address the impacts of irrigation on groundwater ecosystems. We suggest practical steps to mitigate contamination, protect groundwater biodiversity and ecosystem services, and improve irrigation efficiency.

Figure 1.

Unsustainable practices and sustainable irrigation solutions to protect groundwater quality and biota. Source: The figure was created by Biorender.com.

Prioritizing groundwater biota monitoring

First and foremost, general and regular monitoring of groundwater should include monitoring of groundwater biota (Wynne et al. 2021, Hose et al. 2023). The need for routine biological monitoring of groundwaters has been justified on several occasions (Danielopol et al. 2007, Griebler et al. 2010, Di Lorenzo et al. 2024), but it has been rarely implemented in practice (Weigand et al. 2022). Although there is growing interest in studies of groundwater fauna (Koch et al. 2024), regular, systematic sampling of potentially affected and reference areas is needed. Although this task seemed unrealistic three decades ago, today, we can much better assess the composition and trends of groundwater biota and its functions by combining the measures of physicochemical variables, measures of bacterial abundance and microbial activity (Fillinger et al. 2019), and measures of eukaryote communities using an advanced but relatively inexpensive set of molecular tools for barcoding, metabarcoding, eDNA (Tautz et al. 2003, Deiner et al. 2016, Leese et al. 2016, Pawlowski et al. 2018, Weigand and Macher 2018), and functional genomics (Griebler et al. 2014, Anantharaman et al. 2016). In addition, high-quality standardized monitoring is possible using a citizen science approach (Alther et al. 2021, Couton et al. 2023a, 2023b, Korbel and Hose 2024). Therefore, governments should prioritize the development of monitoring of groundwater biota as part of a broader strategy for groundwater protection.

Incorporating aquifer types in monitoring programs

When designing the monitoring programs, different types of aquifers should be considered (Weitowitz et al. 2017). Surprisingly, we are unaware of previous studies that have examined the consequences of irrigation on fauna in karst systems and sinking rivers. Monitoring should directly measure how water abstraction affects groundwater fauna.

Identify multiple sources of groundwater contamination

With monitoring, we should also be able to distinguish and disaggregate different anthropogenic influences that occur concurrently with abstraction and irrigation. The problems associated with the leakage of contaminants often arise from associated activities such as the use of fertilizers, plastics, and phytopharmaceuticals in agriculture (Mammola et al. 2019) or from sources such as untreated domestic and industrial wastewater (Rotiroti et al. 2023). If other anthropogenic disturbances unrelated to irrigation are also present, such as sewage, abandoned or leaking wells, spills, or pasturing, the degradation of groundwater quality may be falsely attributed to irrigation. Conventional detection of contaminants in groundwater cannot identify the main problems for water quality when the signals from agriculture, urbanization, and industry are mixed. This calls for the use of methods that go beyond the standard monitoring, such as passive sampling for emerging contaminants (Cerar and Mali 2016, Mali et al. 2017, Koroša and Mali 2022, Pinasseau et al. 2023), the use of isotopes and tracing of microbial sources to gain a more accurate insight into the sources of groundwater pollution (Ji et al. 2022), which, in turn, allows for better targeting of pollution policies. To properly assess the data collected in the field, the monitoring and study of the large-scale effects of irrigation on groundwater fauna should be complemented by ecotoxicological studies to better define the threshold values for individual pollutants and their mixtures.

Implementation of NSWRMs and appropriate irrigation practices

Many potential risks can be mitigated with the implementation of NSWRMs and appropriate irrigation practices. Novel irrigation systems seek targeted irrigation of crops and thereby minimize water abstraction. Appropriate watering rates and regimes allow plants to fully uptake fertilizers and assimilate them (Fan et al. 2014, Qi et al. 2023), resulting in better agricultural production and the removal of potentially harmful chemicals from the soil (Song et al. 2022). Adequate irrigation therefore not only increases crop production but may also reduce leaching into the soil and may, therefore, keep the groundwater intact. The European Irrigation Association is developing measures to quantify the efficiency of sustainable irrigation but only weakly considers measures of the impact on surrounding ecosystems. Some of these practices have already been encouraged in strategic documents; however, their implementation could be enhanced through the revision of existing groundwater rights to control overabstraction (Young 2014) and through education. Raising awareness and effective communication with municipalities, local communities, water managers, and farmers is needed to put the current progress in sustainable irrigation into practice. In addition, the management of water resources and agricultural land use at the landscape level should be better aligned to ensure a more effective use of the NSWRMs, which should also be implemented in a way that benefits the declining farmland biodiversity (Pe'er et al. 2022).

Implementing targeted irrigation as a last resort for drought resilience

We can expect that droughts and forthcoming climate changes will require a change in agricultural practices. Decision-makers face a challenge of how to protect groundwater resources and secure food production. We propose some check points in the decision-making process. First, environmental conditions must be considered when selecting crop types and strains. Second, NSWRMs that enhance water retention in soil should be mandatory and implemented on a wider landscape level in line with the principles for nature-based solutions, including restoration projects (Cohen-Shacham et al. 2019). Only if the application of NSWRMs does not increase drought resilience to a satisfactory level should irrigation be considered in addition to these precautionary measures. In this case, water sources for irrigation must be carefully selected according to the quantity and quality of the source (surface water, groundwater, proximity to lakes and rivers) and the potential impact of water abstraction on all groundwater dependent ecosystems. All irrigation systems should switch to targeted irrigation, even if it is more expensive. Finally, the status of groundwater should be carefully and frequently monitored during water uptake and after it. It is timely to acknowledge that biodiversity conservation and diverse ecosystem services rely on sustainable farming and vice versa.

Conclusions

The negative impacts of groundwater overabstraction on ecosystems worldwide have been severe. Much of that water has been used in irrigation; however, irrigation is only one of many human practices that modify the water cycle. To minimize our impact on the water cycle and to maximize other ecosystem services, such as drinking water, it is imperative to rethink the use of modern irrigation systems, to develop new technologies, and to reduce or improve the efficiency of existing irrigation areas. If we want to follow the idea of One Health, adoption of a new, sustainable irrigation standard is required to enable the transition of irrigation as an economic activity. The environmental impact of existing irrigation schemes should be reviewed and irrigation systems improved to increase water-use efficiency that will help in protecting local groundwater fauna.

This Viewpoint provides much needed guidelines to mitigate the risk of irrigation on groundwater quality, biodiversity, and ecosystem services. The framework is based on three pillars: regular monitoring of groundwater biota, implementation of NSWRMs, and more efficient irrigation methods, and changes in agricultural practices. This framework can serve as the best currently available guidance for irrigation-related decisions.

Acknowledgments

We thank three anonymous reviewers and editorial board members for constructive criticism of an early version of the manuscript. This study was partially supported by the Slovenian Research and Innovation Agency (grants no. P1-0184, no. P4-0022, no. P1-0020, no. J1-2464, and no. L4-2625), the European Union's Horizon 2020 research and innovation projects OPTAIN (grant agreement no. 862756) and PAPILLONS (grant agreement no. 101000210). The study was also funded by Biodiversa+, the European Biodiversity Partnership under the 2021–2022 BiodivProtect joint call for research proposals, cofunded by the European Commission (grant no. 101052342), and with the funding organizations Ministry of Universities and Research (Italy), Agencia Estatal de Investigación—Fundación Biodiversidad (Spain), Fundo Regional para a Ciência e Tecnologia (Portugal), Suomen Akatemia—Ministry of the Environment (Finland), Belgian Science Policy Office (Belgium), Agence Nationale de la Recherche (France), Deutsche Forschungsgemeinschaft e.V.—BMBF-VDI/VDE INNOVATION+TECHNIK GMBH (Germany), Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Switzerland), Fonds zur Förderung der Wissenschaftlichen Forschung (Austria), Ministry of Higher Education, Science and Innovation (Slovenia), and the Executive Agency for Higher Education, Research, Development and Innovation Funding (Romania); and Biodiversa+, the European Biodiversity Partnership, in the context of the “Sub-BioMon: Developing and testing approaches to monitor subterranean biodiversity in karst” project under the 2022–2023 BiodivMon joint call. It was cofunded by the European Commission (grant no. 101052342) and the following funding organizations: Ministry of Higher Education, Science and Innovation (Slovenia), The Belgian Science Policy (Belgium), Ministry of Universities and Research (Italy), National Research, Development and Innovation Office (Hungary), Executive Agency for Higher Education, Research, Development and Innovation Funding (Romania), and self-financing partner National Museum of Natural History Luxembourg (Luxembourg). GCH was funded by The Australian Research Council (grant no. LP190100927) and by the New South Wales Environmental Trust (grant agreement no. 2019/RD/0027). In addition, support was granted to CG in the frame of the project Stygofauna Austriaca, funded by the biodiversity funds of the Austrian Federal Ministry of Climate Action, Environment, Energy, Mobility, Innovation, and Technology. BS was supported by Texas State University's Faculty Developmental Leave program.

Authors contributions

Cene Fišer, Matjaž Glavan, Rozalija Cvejić, Tanja Šumrada and Maja Zagmajster developed the idea; Cene Fišer prepared the first draft and led the writing; Anita Jemec Kokalj, Nina Mali, Grant Hose, Benjamin Schwartz, Tiziana Di Lorenzo, Christian Griebler and Rozalija Cvejić wrote individual chapters; All authors read, commented on and approved the text.

Author Biography

Cene Fišer ([email protected]), Maja Zagmajster, Anita Jemec Kokalj, Tanja Šumrada, Matjaž Glavan, and Rozalija Cvejić are affiliated with the Biotechnical Faculty at the University of Ljubljana, in Ljubljana, Slovenia. Nina Mali is affiliated with the Geological Survey of Slovenia, in Ljubljana, Slovenia. Grant C. Hose is affiliated with the School of Natural Sciences at Macquarie University, in Sydney, Australia. Benjamin Schwartz is affiliated with the Department of Biology and with the Edwards Aquifer Research and Data Center, at Texas State University, in San Marcos, Texas, in the United States. Tiziana Di Lorenzo is affiliated with the National Research Council's Research Institute on Terrestrial Ecosystems in Florence, Italy; with the National Biodiversity Future Center, in Palermo, Italy; with the Emil Racovita Institute of Speleology, in Cluj-Napoca, Romania; and with the Centre for Ecology, Evolution, and Environmental Changes, the Global Change and Sustainability Institute, and Departamento de Biologia Animal, in the Faculdade de Ciências at the Universidade de Lisboa, in Lisbon, Portugal. Christian Griebler is affiliated with the Department of Functional and Evolutionary Ecology at the University of Vienna, in Vienna, Austria