Cross-cutting story 4: Nutrients

Page Last modified 08 Dec 2022
11 min read
This cross-cutting story explores how food production has driven the wide-scale nutrient pollution of freshwater and marine ecosystems — also impacting human health and wellbeing as a result. The ways in which cross-cutting policy responses address this risk are also investigated.

Nutrients such as nitrogen (N) and phosphorus (P) are fundamental to sustaining plant and animal life on our planet. Undergoing complex chemical and biological changes, nutrients are constantly moved and exchanged, in a cyclical way, in the living and non-living components of the environment. Since the advent of mineral fertilisers, it has become possible to add external N and P inputs to these nutrient cycles. This has led to a strong increase in agricultural production, including in Europe. However, it has also caused nutrient imbalances affecting the environment. Although nutrient concentrations in the environment have generally decreased over the past three decades, excess nutrient pollution remains one of the most serious issues affecting human and ecosystem health in the EU. Impacts include eutrophication, air pollution and climate change.


Sources of human interference with nutrient flows

Nutrient inputs in the European environment originate from a variety of sources, including the atmospheric deposition of nitrogen oxides (NOx) emitted through industrial combustion processes and transport, wastewater releases and discharges from aquaculture production. The major imbalance in N and P cycles, however, arises from diffuse source pollution in agriculture (EEA, 2020a). Its main drivers are the application of mineral fertilisers and manure to agricultural soils, as well as livestock production (Figure 1). For example, only around 60% of the N applied to agricultural land in Europe is taken up by crops (Leip et al., 2011). The rest is released to water, mainly as nitrates (NO3-), or emitted to air as NOx or ammonia (NH3). Agriculture, particularly manure and livestock excreta, is also responsible for 94% of total NH3 emissions in the EU.

Figure 1. Basic diagram of nutrient flows in agriculture

Note: The figure does not show the relative amounts of nutrient flows.

Source: Adapted from Baltic Eye (2016); original illustration by Robert Kautsky/Azote

Box 1. The policy context for nutrient pollution in the European Union

Given the large number of human activities and economic sectors that can affect nutrient cycling, nutrient emissions and their potential impacts on human health and ecosystems are addressed under a number of different policy instruments in the EU. These include:

Reducing nutrient pollution is a central aspect of the EU’s zero pollution action plan and farm to fork strategy. The targets set in these documents include a 50% reduction in nutrient losses, a 20% reduction in fertiliser use and a 25% reduction in the total ecosystem area where air pollution threatens biodiversity. This ambition is also reiterated in the EU biodiversity strategy as a key dimension of the EU nature restoration plan.


Trends in nutrients in Europe

Available data for nutrient-related pressures and concentrations in the European environment show gradual improvement over the past three decades. After peaking in the 1980s, nutrient inputs in agriculture have generally declined due to a drop in mineral fertiliser application, although these trends have levelled off in the past decade and tend to hide significant geographical differences (de Vries et al., 2021). Mineral fertiliser imports are still high: the EU is largely dependent on trade with fertiliser-producing countries such as Algeria, Egypt, Morocco and Russia (EC, 2019). The surplus of N and P inputs on agricultural land in the EU-27, compared with the rate at which these are removed by crops, was estimated to total around 44.4 and 0.8 kilograms per hectare, respectively, in 2014. Relatively high N surpluses are found in intensive livestock regions (de Vries et al., 2021); these include north-western Germany, the Netherlands, Belgium, Luxembourg, Brittany in France and the Po Valley in Italy (as shown in Map 1). 

Map 1. Spatial variation in N surplus (left) and P surplus (right) for the year 2010 in the EU-27

Source: ETC/DI (2022).

Click here to view the figure enlarged

Click here for different chart formats and data

Atmospheric emissions of nitrogen compounds such as NOx and NH3 have gradually declined since 2005. However, the EEA has identified that several EU Member States need to significantly reduce their NH3 and/or NOx emissions to meet their 2030 targets under the National Emission reduction Commitments Directive (EEA, 2022). Overall improvements in urban wastewater treatment and the 2013 EU-level ban on phosphates in consumer detergents have reduced nutrient pollution from point sources in European freshwater bodies, although run-off from agricultural land continues to be a problem. According to data reported to the EEA by EU Member States, the decrease in P concentrations in rivers has been particularly significant. By contrast, nitrate concentrations in rivers and groundwater have remained stable in recent years. From 2016 to 2019, around one quarter of surface water and groundwater stations reported an increase in nitrate concentrations compared with the previous reporting period (EC, 2021a).

According to a recent report, these developments are not enough to fully protect aquatic and terrestrial ecosystems in Europe (ETC/DI, 2022). To do this, further significant reductions in emissions are required (e.g. nutrient run-off would need to be reduced by an estimated 50%). If the contribution of European consumption to N losses in other global regions was factored in, the reduction rate for N inputs in Europe would need to be much higher (EEA, 2020b).


Impacts of nutrient pollution on ecosystems

The leaching and run-off of N and P compounds into surface waters can lead to eutrophication — with high levels of algae and aquatic plant growth, oxygen depletion, aquatic biodiversity loss and reductions in fish populations (Camargo and Alonso, 2006). From 2016 to 2019, surface waters at nearly 36% of river monitoring stations in the EU exhibited eutrophication; a further 19% had nitrate levels that could potentially lead to eutrophication (EC, 2021a). According to Member States’ reporting, nutrient pollution affects 26% of surface water bodies and 17% of groundwater bodies, negatively impacting freshwater habitats and species. Coastal (31%) and marine (81%) waters are also affected by eutrophication (EC, 2021a). The Baltic Sea has the highest proportion of ‘problem areas’ for eutrophication; however, data for the rest of European waters are often lacking (EEA, 2019).

In sensitive ecosystems such as nutrient-poor grasslands and forests, eutrophication can affect species diversity and plant species’ richness and facilitate new species invasions. When acidification has an impact on freshwater and terrestrial ecosystems, plant and fish species may be affected as the pH of soils and water decreases and toxic metals leach from the ground. Despite some improvements between 2005 and 2019, N deposition levels remain significantly above the critical loads for eutrophication, i.e. the levels above which ecosystems are adversely affected.


How is human health affected?

Excess nutrient pollution has a negative impact on several health-related ecosystem services, including water and air quality, food and water provision and recreational activities such as fishing and bathing (de Vries, 2021). High nutrient concentrations in surface waters can proliferate cyanobacteria, also known as blue-green algae as explained in the zero pollution ‘Signal’ on cyanobacteria. When nitrate and nitrite-contaminated groundwaters are used for drinking water, they may also cause methemoglobinemia — a condition that affects the blood’s capacity to carry oxygen to tissues, which is particularly dangerous in babies. In the EU, 14% of all groundwater monitoring points reported nitrate concentrations exceeding the threshold of 50mg/l during 2016-2019 (EC, 2021). Comparing this with data from the previous reporting period shows no evidence of a downwards trend (EC, 2018).

NH3 emissions are also problematic because of their link to air pollution. NH3 is a precursor of PM2.5 (fine particulate matter), which represents the single biggest environmental health risk in the EU as detailed in the zero pollution assessment on health.


The need for cross-cutting policy responses

Historical reductions in nutrient inputs, concentrations of N and P in freshwater bodies and atmospheric emissions of N compounds suggest that policy responses and more efficient farming practices are helping to reduce excess nutrient pollution in Europe. However, additional measures are needed to meet the EU’s nutrient-related 2030 targets. Given the multi-faceted nature of nutrient pollution, these measures must be cross-cutting.

In the EU, it is important to fully implement existing legislative obligations (in contrast to the present insufficient implementation and enforcement of the Nitrates Directive (EC, 2021a) and the Urban Wastewater Treatment Directive (EC, 2020)). In addition, Member States will need to go above and beyond what is presently required. For example, many measures to improve nutrient management in agriculture (such as restricting the application of N fertilisers) are mandatory in the ‘nitrate vulnerable zones’ that Member States must identify under the Nitrates Directive. It would also be beneficial if these measures were extended to other areas where it may be possible to further reduce N inputs without harming crop production. For example, more nuanced farming methods such as precision fertiliser application can reduce both costs and nutrient losses (Blasch et al., 2022). Similarly, Member States could consider investing in innovative wastewater treatment techniques and nature-based solutions to reduce nutrient discharges from point sources.

More fundamentally, closing the nutrient cycle may need to go hand in hand with structural attempts to transform food systems (EEA, 2020a; Billen et al., 2021). This transformation could include dramatically scaling up agroecological practices and reducing livestock densities in regions where improvements in nutrient management are insufficient to stay within critical loads (Schulte-Uebbing and de Vries, 2021). The transformation would also require greater emphasis on circularity, including reducing fertiliser imports and increasing the reuse of locally available manure. Lastly, various studies have indicated that an EU-wide shift to healthier diets based on reducing meat and dairy consumption would also yield significant environmental benefits in terms of lower N losses (e.g. Westhoek et al., 2015). 


Baltic Eye, 2016, Nutrient recycling in agriculture — for a cleaner Baltic Sea, Baltic Sea Centre Policy Brief (!/menu/standard/file/PBgödselENGwebb.pdf) accessed 27 October 2022.

Billen, G., et al., 2021. ‘Reshaping the European agro-food system and closing its nitrogen cycle: the potential of combining dietary change, agroecology, and circularity’, One Earth 4(6), pp. 839-850 (

Blasch, J., et al., 2022, ‘Farmer preferences for adopting precision farming technologies: a case study from Italy’, European Review of Agricultural Economics 49(1), pp. 33-81 (

Camargo J. A. and Alonso A., 2006, ‘Ecological and toxicological effects of inorganic nitrogen pollution in aquatic ecosystems: a global assessment’, Environment International 32, pp. 831-849 (

de Vries, W., 2021, ‘Impacts of nitrogen emissions on ecosystems and human health: a mini review’, Current Opinion in Environmental Science and Health, 21, 100249 (

de Vries, W., et al., 2021, ‘Spatially explicit boundaries for agricultural nitrogen inputs in the European Union to meet air and water quality targets’, Science of the Total Environment 786, 147283 (

EC, 2018, Report from the Commission to Council and the European Parliament on the implementation of Council Directive 91/676/EEC concerning the protection of waters against pollution caused by nitrates from agricultural sources based on Member States reports for the period 2012-2015 (SWD (2018) 246 final of 4 May 2018) ( accessed 25 October 2022.

EC, 2019, Fertilisers in the EU: prices, trade and use, EU Agricultural Markets Brief No 15, European Commission ( accessed 16 June 2022.

EC, 2020, Report from the Commission to the European Parliament, the Council, the European Economic and Social Committee and the Committee of Regions ‘Tenth report on the implementation status and programmes for implementation (as required by Article 17 of Council Directive 91/271/EEC, concerning urban waste water treatment’ (SWD (2020) 145 final of 10 September 2020) ( accessed 25 October 2022.

EC, 2021, Commission Staff Working Document accompanying the document ‘Report from the Commission to the Council and the European Parliament on the Implementation of Council Directive 91/676/EEC’ (SWD(2021) 1001 final of 11 October 2021) ( accessed 25 October 2022.

EEA, 2019, Nutrient enrichment and eutrophication in Europe’s seas: moving towards a healthy marine environment, EEA Report No 14/2019, European Environment Agency ( accessed 25 October 2022.

EEA, 2020a, Water and agriculture: towards sustainable solutions, EEA Report No 17/2020, European Environment Agency ( accessed 25 October 2022.

EEA, 2020b, Is Europe living within the limits of our planet? An assessment of Europe’s environmental footprints in relation to planetary boundaries, Joint EEA/FOEN Report, EEA Report No 01/2020, European Environment Agency ( accessed 25 October 2022.

EEA, 2022, National Emission reduction Commitments Directive reporting status 2022, EEA Briefing, European Environment Agency ( accessed 27 October 2022.

ETC/DI, 2022, Impacts of nutrients and heavy metals in European agriculture: current and critical inputs in relation to air, soil and water quality, ETC-DI Report 2022/01, European Topic Centre on Data Integration and Digitalisation ( accessed 25 October 2022.

Leip, A., et al., 2011, ‘Farm, land, and soil nitrogen budgets for agriculture in Europe calculated with CAPRI’, Environmental Pollution, 159, pp. 3242-3252 (

Schulte-Uebbing, L. and de Vries, W., 2021, ‘Reconciling food production and environmental boundaries for nitrogen in the European Union’, Science of the Total Environment 786, 147427 (

Westhoek, H., et al., 2015, Nitrogen on the table: the influence of food choices on nitrogen emissions, greenhouse gas emissions and land use in Europe, ENA Special Report on Nitrogen and Food, Centre for Ecology and Hydrology ( accessed 25 October 2022.


Cover image source: © Matjaz Krivic, Well with Nature /EEA


Geographic coverage


Filed under:
Filed under: nutrients
Document Actions