Defra Project WQ0112

UNDERSTANDING THE IMPACT OF FARMING ON AQUATIC ECOSYSTEMS

Final Report 31 January 2008

Andrew Davey1

Mike Gardner1

Ian Johnson1

Stephen Nixon1

Michael Payne2

Holly Smith1

1WRc plc, Frankland Road, Blagrove, Swindon, SN5 8YF

2 Michael Payne Environmental Consultants, Field Barn Farm, Boughton, Kings Lynn, PE33 9AH

Table of contents

1Introduction

1.1Rationale

1.2Aims and objectives

1.3Scope of review

1.4Approach

1.5Trends in agricultural production and potential impacts on aquatic ecosystems

2Impact of pollutants on aquatic ecosystems

2.1Nitrate/nitrogen

2.2Phosphorus

2.3Ammonia

2.4Soil sediment

2.5Pesticides

2.6Veterinary medicines

2.7Faecal pathogens

2.8Organic material

2.9Endocrine disrupting chemicals

2.10 Other pollutants

2.11 Combined effects of different pressures

3Indicators of pollution

3.1Background

3.2Species/biological quality elements indicative of the effects/impacts of farming

3.3Monitoring under the Water Framework Directive

3.4Use of biomarkers as early warning systems for farming-related activities

3.5Summary

4Understanding the impact of farming on aquatic ecosystems

4.1Introduction

4.2Knowledge of activities, pathways, processes, source apportionment and impacts

4.3Quantification of scale and importance of impact

4.4Improvement, development and implementation of cost-effective mitigation measures

5Knowledge transfer plan

6References

1

1Introduction

1.1Rationale

The Water Framework Directive (WFD), which came into force on 22 December 2000, is a wide ranging piece of European environmental legislation that sets objectives for protecting and enhancing water quality and the status of aquatic ecosystems. Specifically, it aims to achieve “good chemical and ecological status” in surface waters (rivers, lakes, transitional(estuarine) and coastal waters) by 2015, where "good" represents a slight deviation from minimally impacted reference conditions. To achieve this, the WFD makes provision for the establishment of River Basin Districts (RBDs) within which river basin management plans will be implemented to target both point and diffuse sources of water pollution.

Farming activities are major sources of pressures on the water environment. The development and deliveryof cost-effective measures to meet the objectives set out by the WFD requires an assessmentof the contribution that agricultural land management practices makes to pollutant losses to water. In addition, the impact of those pollutants on the ecology of the receiving waters must be understood and quantified. In 2002, Defra conducted a Strategic Review of diffuse water pollution from agriculture in England, which assessed the environmental pressures and impacts exerted on water by agricultural practices and critically appraised the success of existing policy instruments to control such pollution[1]. While some of the impacts of pollution are well documented (e.g. eutrophication), there is now a need to pull together information on the effect of a wider range of pollutants across all types of aquatic ecosystem.

This report summarises the main findings and conclusions from the study. It is accompanied by two Annexes with more detailed background information on some of the key aspects: sources and pathways of pollutants, and strategies to tackle agricultural water pollution are covered in Annex A, and indicators of pollution are covered in Annex B.

1.2Aims and objectives

The aim of this report is to explore and benchmark current knowledge and understanding of the effects of farming on aquatic ecosystems in England and Wales and to identify future research needs. To achieve that aim the Defra Tender document indicated that the desk study should address the following points:

  • The study should identify what data/information already exists, where it resides and how readily available it is.
  • It should focus on the impact of pollutants/contaminants, including sediments, at the aquatic ecosystem level and on individual species, including vertebrates, invertebrates and algae etc.
  • Existing knowledge on suitable indicator species for the effects of pollution/contamination, including those that could act as early warning markers, should be collated and discussed.
  • Knowledge on the sources and exposure pathways of potential pollutants, and the relative contribution and effects of different farming management practices, should be discussed to provide context and background for the study.
  • Recommendations for future R&D on the effects of farming on aquatic ecosystems should be proposed, and should focus in particular on research which could be used to identify cost-effective mitigation approaches.
  • A knowledge transfer plan should be included. It is important to identify clearly the outputs and pathways to delivery from the proposed project.

1.3Scope of review

Farming is defined as all agricultural and horticultural activities. Agriculture uses over 76% of the land area of England and Wales and horticulture is undertaken on around 1% of the total agricultural land in the UK.[2] The main categories of pollutantarising from agricultural activities are:nitrate; ammonia; phosphorus; soil sediment; pesticides;veterinary medicines;faecal pathogens; organic material; endocrine disrupting chemicals; other hazardous substances such as heavy metals and hydrocarbons; and hydromorphological pressures such as land drainage, flood defence and water abstraction. Hydromorphological pressures thatdirectly impact ecosystems and indirectly affect water quality are not discussed in detail in this review.

This report reviews the impact of agricultural pollution on all surface waters (rivers, lakes, transitional and coastal waters). Groundwater provides base flow to many rivers and lakes and is an important transport pathway for pollutants such as nitrates. The importance of groundwater in the achievement of Good Ecological Status (GES) in dependent surface water bodies is recognised by the inclusion of ‘connection to groundwater’ as a quality element for the classification of the status of river and lake water bodies. The role of groundwater in modifying water quality and ecology is therefore integrated across all surface water body categories rather than considered separately.

Further details of the scope of the review are provided in Annex A.

1.4Approach

The report collates and assimilates data and information from sources including: Defra research projects (searched via Defra Environment Agency technical reports and science reports, UKTAG reports and guidance notes (searched via and WFD Article 5 risk assessment reports and technical methods (available at In addition, a full CSA ( search was conducted for relevant journal articles and scientific reports using three keyword searches:(1) to search for information on the sources and exposure pathways of pollutants we used the following terms: agriculture, pollution, water quality, source, transport, pathway, diffuse pollution, run-off, agriculture, UK; (2) to search for information on the impact of these pollutants on aquatic ecosystems we used the following terms: pollution, water quality, impact, effect, stress, ecology/ecological, species, population, community, toxicity, river, lake, estuary, coast, freshwater, marine, UK; (3) to search for information on indicators that are used to assess the extent and intensity of pollution we used the following terms: (iii) pollution, water quality, bioindicator/biological indicator, impact assessment, indicator species, index/metric, river, lake, estuary, coast, freshwater, marine, UK.

A full reference list is provided in Section 6, where the availability of these documents is flagged.

1.5Trends in agricultural production and potential impacts on aquatic ecosystems

Studies have been undertaken to assess how the reform of the EU’s Common Agriculture Policy and other policies will impact on farming and water quality. Some of the main predicted changes and projections to 2015 relevant to potential impacts on aquatic ecosystems include:

  • Overall land use will not change markedly;[3]
  • Changes in farming practices will help reduce levels of nitrate and phosphorus in surface and ground waters;[4]
  • The per hectare applications of fertiliser and sprays unlikely to change markedly;[5]
  • Extensification of grassland utilisation is likely to lead to reduced fertiliser applications;[6]
  • Marked reduction in livestock numbers;[7]
  • Fewer larger herds of dairy cows – disappearance of mid-sized herds, focus of production will be in the lowlands. Pressures of dairying will be concentrated in specific areas (more slurry to be stored).[8]. In some parts of country (South West) the size of herds is already increasing;[9]
  • Reductions in livestock numbers are likely to lead to reductions in levels of veterinary medicines in water bodies in main livestock regions e.g. South West and West Midlands – though intensification of dairying in parts of these regions may see an increase in localised areas;[10]
  • Fewer sheep will mean a reduction in sheep dip use;[11] and
  • Fewer cattle and sheep will reduce problems with poaching[12] and potential soil erosion;
  • Outdoor pig sector to increase to escape from measures required under IPPC Directive for installations for the intensive rearing of pigs (and poultry).[13]

Climate change will have a significant effect on agriculture and potentially its impact on aquatic ecosystems. Defra summarises the direct threats from climate change as prolonged and more frequent droughts; changes in rainfall distribution; more storms and other extreme events; rising sea levels; increased and changing pest loads; increased risk of heat stress in livestock farming; and, possible changes in soil water balance.[14] Increasing temperatures and hence growing seasons may also lead to new crops being grown. Other predicted impacts include: increased/change in range of native/alien pest and disease problems[15] (leading to the use of more or different pesticides); increased use of irrigation[16] (increased abstractions in some catchments); increased soil erosion (increased sediment loads to water bodies); changed poaching/water logging risk in some areas (changes in pollutants pathways and increased sediment load). Changes in intensity and seasonality of rainfall and increased temperatures may change the fate and behaviour (and hence impact) of pesticides though the overall effect may be very variable and difficult to predict.[17]

The likely scale of the changes to agriculture that would be required to achieve good ecological status (GES) for the WFD in terms of nitrate and phosphorus has been modelled.[18] The results predict that the achievement of GES would require substantial changes in agricultural land use and management. These might include identification of high risk areas where the risk of nutrient export is high, controls on fertiliser use and livestock densities, and taking sensitive areas out of production. For example, total nitrogen fertiliser usage and livestock numbers have declined in recent years and could be expected to reduce agriculture’s contribution to water pollution.[19] However, other changes, such as the continuing trend towards intensification, are likely to counteract this to some extent.

A more detailed description of sources and pathways of pollutants, and strategies to tackle agricultural water pollution, is given in Annex A to this report.

2Impact of pollutants on aquatic ecosystems

This section reviews, for each of the ten pollutant categories listed in section 1.3, the key sources and pathways, the magnitude of source and exposure pressure (including an assessment of the proportional contribution from farming), the potential impact on aquatic ecosystems, and the current extent and intensity of impact.

In assessing the extent and intensity of the impact of farming on aquatic ecosystems, the report draws heavily on the results of the Environment Agency’s (EA) WFD Article 5 risk assessments, which identify those water bodies at risk of failing to achieve the WFD objectives, such as the achievement of good ecological and chemical status due to different categories of pressure. The risk assessments give an indication of the potential impact of agriculture on the ecological status of water bodies. However, water bodies were often identified as being at risk from more than one pressure making it difficult to apportion the impact arising from agriculture from that arising from other activities and sectors. Also some of the risk assessments were based on modelling rather than on direct evidence of ‘impact’ on ecological status. Therefore, even though the risk assessments identify the potential scale of the impact of agriculture on ecological status, the actual impact may not have been fully quantified.The UK Technical Advisory Group on the Water Framework Directive (UKTAG) has proposed environmental standards for the implementation of the WFD and has assessed the implications of applying them to existing monitoring data in terms of achievement of good ecological status.[20],[21] These results are also referred to in the text below as appropriate. The first full classification of ecological status of water bodies will be available in December 2008 when draft River Basin Management Plans will be published.

2.1Nitrate/nitrogen

The principal farming activities leading to the pollution of water bodies by nitrate is the application of inorganic fertilisers and animal manures to arable and pastoral land. Nitrate is highly soluble andis readily leached from soils in water bodies via cracks and preferential (subsurface) pathways.[22] It can also directly enter water bodies via run-off from land and through atmospheric deposition of NOx and ammonia: the latter is rapidly oxidised when deposited on land. Nitrates lost from farmland may often be accompanied by other agricultural pollutants which may compound the impact on ecology, for instance nitrates lost from fertilisers and slurries applied to land are often accompanied by soil sediment and organic matter. Unlike phosphorous, however, nitrate is unlikely to be incorporated with soil sediments due to its high solubility.

At the national level (England and Wales) agriculture is the predominant source (60.6% in 2000/2001) of the total nitrogen load to all surface waters,with 32.1% coming from sewage treatment works.[23]Total nitrogen loads to sea showed no clear trends between 1991 and 2003.[24]There are clear regional differences with agricultural areas such as the South West and Anglian regions having the highest nitrogen loads from agriculture while more populous areas such as the Thames region have a higher proportion of nitrogen loads arising from sewage treatment works.

The EA’s WFD Article 5 risk assessments estimated that 37.9% of river water bodies (45.0% by length), 19.9% of transitional water bodies (8.5% by area) and 13.1% of coastal water bodies (4.9% by area) were at risk from diffuse nitrogen inputs.[25][26] The risk assessment for rivers included nitrogen inputs from agriculture and atmospheric deposition but did not consider any ecological effects of nitrogen enrichment. For transitional and coastal waters, diffuse (riverine) inputs and direct discharges were considered with no specific apportionment for agricultural inputs. No risk assessment was undertaken for diffuse nitrogen in lakes.

As of 2007 there are 137 sensitive areas in England and Walesdesignated under the Urban Waste Water Treatment Directive as being eutrophic or likely to become eutrophic in the near future without action being taken. These sensitive areas are a mixture of rivers, lakes (reservoirs), harbours and estuaries, and hence there will be a mixture of which nutrient will be most pertinent (nitrogen and/or phosphorus) in terms of ecological impact and actions required. One of the criteria for the identification of polluted waters under the Nitrates Directive is whether waters are eutrophic or will become eutrophic in the near future without action being taken. As a result, a total of 55% of England was designated as a Nitrate Vulnerable Zone (NVZ) in October 2002 though not all were necessarily designated because of the eutrophication criteria. Defra is currently reviewing and consulting on increasing NVZs to 70% of England or applying the Action Programmes required under the Directive to the whole of England. This latest review recognises that nitrogen may also play a role in the eutrophication of freshwaters. There are also 12 problem or potential problem areas identified under OSPAR's comprehensive procedure for the assessment of eutrophication. These are estuaries, bays or harbours and correspond to areas designated under there UWWT and/or Nitrates Directive.

Nitrate concentrations are high in water draining from much of the agricultural land in England.[27] For example in 2006, 28% of rivers had high concentrations of nitrate (greater than 30mg l-1)[28] with the highest concentrations being found in the Midlands, Anglian and Thames regions, which have some of the largest areas under intense agricultural production. Similarly, a review of nitrate concentrations in rivers in England between 1999 and 2004 reported that the mean nitrate concentration varied regionally from 15 mg l-1 in North West region to 39 mg l-1 in Anglian region.[29] Typically, nitrate concentrations are higher in lowland areas dominated by arable agriculture than in areas dominated by pastoral farming[30] and lower in wetter areas where high quantities of rainfall dilute the nitrate within soils before being leached or washed into water courses.[31] Concentrations in drainage waters from grassland systems are highly variable depending upon the intensity of stocking and management.[32] Nitrate concentrations are increased where manures are used, even under ‘best practice’.

The implications of the proposed WFD environmental standards for dissolved inorganic nitrogen have been recently assessed.[33] Of the 60 transitional and coastal water bodies with sufficient monitoring data, 65% (by number) would be classified as less than good ecological status. There are 136 transitional and 99 coastal water bodies identified for the WFD, and hence this initial classification may not be fully representative of all water bodies.

Nitrate occurs naturally in all surface waters but elevated concentrations of nitrate can cause deterioration of ecological quality in three main ways: eutrophication, acidification and toxic effects.

Eutrophication:Nutrients (e.g. nitrogen and phosphorus) in the appropriate amounts (i.e. background levels) are essential to maintain an adequate primary productivity, which in turn is essential to support higher trophic levels and to maintain a healthy ecosystem structure and function. In general, excessive nutrients of anthropogenic origin cause an increase in plant growth (eutrophication), which in still waters causes increased phytoplankton biomass, often dominated by harmful or toxic species, leading to increased turbidity and decreased light transparency. In rivers this may be seen as increased attached algal growth or even excessive growth of higher plants. In estuaries and coastal waters, excessive growth of opportunistic macroalgal species can result in the formation of dense algal mats, which reduce light penetration to submerged communities and cover intertidal sediments. Sea grasses may also experience severely retarded growth as a result of the growth of opportunistic macroalgal species.[34]These are examples of the direct effects of nutrient enrichment. As a consequence of increased plant growth, there is an imbalance between the processes of plant/algal production and consumption, followed by sedimentation of organic matter, stimulation of microbial decomposition and oxygen consumption with depletion of bottom-water oxygen in stratified water bodies (indirect effects). Thus, eutrophication causes not only nuisance increases in plant growth but also adverse changes in species diversity as well as reduced suitability for human use and consumption.