Prevention of environmental pollution from agricultural activity: guidance

Code of good practice, giving practical advice to farmers and others on minimising pollution.

Section 2: diffuse agricultural pollution


*1. All cropped land over the following winter must, where soil conditions after harvest allow, have either: crop cover, grass cover, stubble cover, ploughed surface or a roughly cultivated surface. Fine seedbeds must only be created very close to sowing. [GAEC measure 1]

2. Protect your soil by following the guidance in this Code regarding preventing damage and erosion.

3. Follow "The 4 Point Plan", which offers guidance on how to:

  • reduce dirty water around the farm

  • improve nutrient use

  • carry out a land risk assessment for slurry and manure

  • manage your water margins

4. Use buffer strips and other measures to reduce surface run-off from fields.

5. Carefully plan all storage and handling arrangements for livestock slurries and manures, animal feedstuffs, silage effluent, agricultural fuel oil, dirty water, fertilisers, veterinary medicines, chemicals and pesticides at your farm.

6. Maintain a suitable distance from any watercourse including ditches (e.g. 10m) or drinking water supplies (e.g. 50m), especially when handling or applying fertilisers, organic wastes, pesticides or other chemicals.

7. Think about ways to protect and enhance your local environment, and how to minimise the impacts of diffuse agricultural pollution of water, land and air.

8. Account for every input, especially of nutrients, pesticides and other chemicals through careful planning.

9. Ensure that any biobed, reedbed, wetland or infiltration system installed to reduce the risk of diffuse pollution is discussed with SEPA before it is constructed.

10. Obtain specialist advice when considering using wetlands, ponds or infiltration systems to treat contaminated roof or dirty yard run-off at the farm steading.

11. Adopt "good housekeeping" and waste minimisation practices that aim to prevent pollution at source.

12. Minimise the area of farmyard and roads over which animals can excrete and over which equipment transporting slurry is moved. Take steps to control the run-off from these areas.

13. Ensure sprayer operators are fully trained and posses certificates of competence and that sprayers are properly maintained and regularly tested.


1. Don't allow the runoff from roads, farmyards, hard standings and ring feeder areas used by stock to discharge directly to a watercourse.

2. Don't allow livestock to have access to watercourses. Instead, provide water at drinking troughs wherever possible.

3. Don't employ any agricultural contractor or company involved in spreading organic waste to land unless they are competent and suitably trained, aware of legal requirements and are willing to follow the guidance in this Code.

4. Don't use pesticides, veterinary medicines or chemicals unless there is an identified need.

5. Don't allow the rainwater from poultry buildings that are ventilated to the roof to discharge directly to a watercourse.

6. Don't directly overspray a watercourse when using pesticides.

7. Don't hesitate to get involved in catchment partnerships to address diffuse agricultural pollution.

8. Don't forget that over-abstraction of irrigation water from watercourses can cause downstream water pollution.

What is diffuse agricultural pollution?

2.1 For the purposes of this Code, diffuse agricultural pollution is contamination of the soil, air and water environments resulting from farming activities. This pollution tends to arise over a wide geographical area and is dependent on what happens on the surface of the land. Although individually minor, such pollution on a catchment scale can be significant, considering the cumulative effect which these separate discharges can have on the environment. Activities such as ploughing, seedbed preparation, crop spraying, fertiliser spreading and applying slurry may all contribute to diffuse pollution. Run-off from farm roads and yards, the surface of fields and dusty roofs after rainfall are all potential sources of pollution. There is therefore a wide range of potential diffuse pollution sources which are associated with farming practices and which can harm the environment.

Why is it important?

2.2 Maintaining a high quality environment in Scotland is essential for marketing high quality agricultural products. This link is one of Scotland's strengths and should be at the heart of every successful farming business.

2.3 Water quality in Scotland is generally good, and adherence to good agricultural practice is on the increase. Nevertheless, there are areas of concern. SEPA considers that diffuse agricultural pollution is now the most significant cause of poor river quality in certain parts of Scotland and that it will continue to be unless appropriate action is taken at individual farm and catchment level to turn the situation around.

2.4 Losses of nutrients or agrochemicals to land or water represent not only a financial loss to farming but can also damage the environment. By applying these inputs in the right amounts and at the right time both farmers and the environment can benefit. Excess nutrients, such as nitrogen and phosphorus, can harm soils, rivers, lochs and estuaries by causing algal blooms and by changing the natural balance of plants, insects and other life. In the wrong place, pesticides can kill river insects and fish and can remain in river sediments for many years. Run-off from dirty yards, roads and grazing fields or land that has been spread with livestock slurries can also contribute to the bacterial contamination of inland and coastal waters and the failure of environmental quality standards. Fellow farmers downstream may experience poor quality water or incur extra expense in dealing with the effects of diffuse pollution including the possibility of disease transmission. In addition, groundwater (i.e. water held below the surface of the land; an important source of drinking water in rural areas) can be put at risk as a result of the leaching or percolation of nutrients and pesticides from the surface of the land. Groundwater is also important in maintaining river flow and for other aquatic environments. If it becomes polluted, surface waters are also at risk.

2.5 The total effect of a number of individually minor sources of contamination can be highly significant over an entire catchment area. If the sources of water for a river are predominately contaminated, then the whole river is likely to be polluted. Small watercourses, with little dilution, are more likely to be adversely affected by diffuse pollution than larger rivers. Over abstraction of irrigation water from watercourses can exacerbate this problem by lessening the potential for dilution. However, diffuse sources of nutrients can also affect groundwater or large water bodies, especially lochs which have low levels of plant nutrients naturally.

2.6 Measures to reduce the risk of pollution at the farm steading (for example, improved collection and storage of silage effluent, slurry, fuel oil and pesticides) have successfully reduced the risk of direct discharges to rivers. Attention is now increasingly being focused on the activities being carried out in the fields.

What legislation must be complied with?

2.7 The Water Framework Directive was agreed in December 2000 and a comprehensive and co-ordinated programme has begun to be implemented to protect and improve the water environment in Scotland. This Directive dovetails with the requirements of those Directives that are not repealed by it, such as the EC Nitrates Directive. The Directive was transposed into Scottish primary legislation through the Water Environment and Water Services (Scotland) Act 2003. Secondary legislation, the Water Environment (Controlled Activities) (Scotland) Regulations, is being developed under this Act to give effect to the range of controls necessary to protect the water environment.

2.8 The new regime will be underpinned by a participative river basin management planning process, under which the full range of potential threats to the aquatic environment will be considered. A series of risk-based controls will be gradually introduced during 2006 and 2007 which will address diffuse pollution; point-source pollution; abstraction; impoundment and river engineering. Many of the standards that farmers will be expected to follow will be based on existing Codes, such as this PEPFAA Code, and on recognised good practice.

What types of diffuse agricultural pollutants are there?

2.9 Diffuse agricultural pollution is principally associated with:

  • soil particles

  • pesticides and other potentially toxic chemicals, including veterinary medicines

  • nutrients, principally nitrogen and phosphorus

  • pathogens, for example, bacteria from livestock slurries and manures spread on land and run-off associated with intensive grazing practices

  • gases such as ammonia

Soil particles

2.10 Soil is effectively a non-renewable resource due to the time it takes to be formed. It should therefore be protected from damage or loss in order to sustain agricultural production, as well as for the life it supports in itself. In addition, soil and water quality are very closely linked. Eroded soil from grazed or cultivated land, muddy run-off from farm roads or yards and via field drains can cause environmental problems such as destroying gravel riffles on the bed of watercourses. These riffles are an essential habitat requirement for many aquatic insects and provide spawning areas for fish.

2.11 Soil particles are also important because they can carry more serious pollutants. For example, some pesticides bind firmly onto soil particles and are therefore liable to contaminate watercourses when soil is lost from fields. Similarly, mud on farmyards and roads may carry oily residues. Phosphorus can be lost from farmland to water and can cause pollution. In excess, certain trace elements transported with the soil can also damage the aquatic environment. It should also be remembered that erosion very often involves the loss of the most fertile soil from a field.

Pesticides, sheep dips and other toxic chemicals

2.12 Pesticides can exert damaging effects on river habitats and water resources. Should pesticides be required, seek specialist advice on the options that are available. Once it is determined that a pesticide is to be applied, the label recommendations must be followed. The adoption of Crop Protection Management Plans (CPMPs) or precision farming can assist in optimising inputs and minimising risks.

2.13 If poorly managed or controlled, pesticides in tank rinse waters from the cleaning of protective clothing, or from residues in bags or containers, can cause pollution. Due to the particular risks that arise during pesticide handling and washdown operations, consideration should be given to the installation of a purpose-built or specially designed area that drains to, or that is situated directly over, a biobed. Guidance on the design of such areas is available from the Crop Protection Association (CPA) under "The Voluntary Initiative" (VI).

2.14 It is also essential to avoid spraying pesticides in conditions or circumstances where drift can occur. Buffer strips or unsprayed headlands should be considered prior to spraying fields bordered by watercourses or ditches. Farmers and contractors should never directly overspray watercourses. Farmers must carry out a "Local Environmental Risk Assessment for Pesticides" (LERAP) if they want to reduce the 5m aquatic buffer strip. This is dependent upon:

  • the size of the watercourse bordering the land being sprayed (in respect of horizontal boom sprayers)

  • the pesticide being applied using certain nozzle types and/or reduced doses

  • whether the product qualifies for the LERAP scheme

2.15 A very wide range of chemical compounds are used as pesticides and each of these interacts with soils and water differently. Some will move through soil quite easily and enter groundwater. Such water may then be abstracted for use in public or private drinking water supply, or in food processing etc. Once present in groundwater, pesticides can be present for many years and are very costly to remove. It is therefore important that such chemicals are prevented from entering groundwater in the first place.

2.16 The chemicals used in sheep dip are also highly toxic, and can have potentially devastating effects on aquatic life over large distances. They can also pollute groundwaters. Each aspect of the dipping operation must be planned in advance, all possible pollution risks must be identified and action must be taken to minimise these risks as far as possible. Farmers should take note of the guidance on good sheep flock management given in section 8 of this Code. Staff should be suitably trained in the correct use of dips and dipping practice. SEERAD has issued guidance for those involved in dipping sheep, in the form of "The Sheep Dipping Code of Practice for Scottish Farmers, Crofters and Contractors" under the Groundwater Regulations 1998 (available from SEERAD and also via the Scottish Executive's website). Waste sheep dip disposal may only be undertaken in accordance with an authorisation issued by SEPA. It is also possible for dip to be disposed of off farm, through a licensed waste contractor. Note that the Groundwater Regulations 1998 must be complied with to be eligible for the Single Farm Payment.

2.17 Sewage sludge or industrial wastes can contain potentially toxic substances such as heavy metals and persistent organic chemicals which may contaminate soil and pollute rivers. Certain precautions must be taken and statutory obligations complied with. Analysis of the waste before use, assessing the land suitability prior to spreading, calculation of the growing crop requirements, soil sampling and nutrient budgeting can all reduce the risk of diffuse agricultural pollution occurring. The waste producer or their contractor may carry out some, or all, of this work for farmers. Anyone wishing to apply industrial wastes to agricultural land must demonstrate in advance, and to SEPA's satisfaction, that such an application will result in benefit to agricultural or ecological improvement. Note that the statutory controls on the application of sewage sludge to agricultural land must be complied with to be eligible for the Single Farm Payment.

2.18 Particular risks may arise when organic wastes are injected into drained land, especially over gravel backfill.


2.19 If leached in excessive amounts, nutrients such as nitrogen (N) and phosphorus (P) can cause severe problems for rivers, lochs, estuaries and coastal waters by, for instance, contributing to the development of toxic algal blooms or foul smelling mats of algae on our coastline. Nutrients can be lost from manures and slurries as well as from other organic wastes spread on land, and significant losses can also be associated with fertilisers and soil. Advice must be tailored to the particular farm and catchment area in order to prevent such losses and reduce the risk of pollution.

2.20 Nitrogen-based fertilisers are used in significant amounts in both arable and livestock farming. Water passing through the soil dissolves salts, nutrients and organic substances. When these materials are carried out of root range by water draining through the soil, they are said to have "leached". Nitrate (from inorganic nitrogen fertilisers or derived from organic manures) is leached especially rapidly because it is very soluble. This is particularly the case during rainfall if nitrogen fertiliser has been over-applied and the soils themselves are free draining. In areas where there are sandy soils overlying permeable rocks, there are particular risks of nitrate leaching into groundwater.

2.21 The key to preventing diffuse pollution by nitrate is to ensure that all inputs are carefully accounted for and that any applications are made to meet the requirements of the growing crop. Farmers in the Nitrate Vulnerable Zones (NVZs) are obliged to comply with an Action Programme, including limits on nutrient applications, adherence to closed periods and record keeping. These requirements must also be complied with to be eligible for the Single Farm Payment.

2.22 Soil erosion is usually the major contributory factor to losses of phosphorus (P) to freshwater. Phosphorus can also reach rivers as dissolved P from field drains and as suspended solids in some soils. It is important therefore not to allow soils to become excessively high in this nutrient. Soil sampling is recommended to assess P levels prior to determining the application rate of fertilisers and manures.

Manures and slurries

2.23 Livestock slurries and manures, and other organic wastes, are valuable materials for improving soil fertility and can save on fertiliser costs. However, they are highly polluting if spread at the wrong time or in the wrong place. They can also be associated with the microbiological contamination of rivers and groundwater if insufficient precautions are taken.

2.24 Adverse effects can also arise from allowing livestock access to watercourses by direct excretion and damage to riverbanks by poaching. This could affect the health of your fellow farmers' livestock downstream if they drink this contaminated water. Wherever possible, install water troughs and fence off watercourses to eliminate this problem. It is essential to ensure that public and private drinking water supplies are protected from grazing animals and landspreading activities.

2.25 Field middens must also be sited at least 10 metres from a watercourse and not where they can contaminate field drains. 

2.26 The area of farmyard and roads over which animals can excrete, and equipment operates to transport slurry, should be minimised.

2.27 In vulnerable locations, the drainage from stored manures and slurries or the seepage from housed livestock units can be highly polluting to surface and groundwaters.

2.28 Apart from the nutrient content and high organic loading, the possibility of microbiological contamination can threaten rivers, bathing waters and individual groundwater sources and affect compliance with environmental quality standards often associated with EC Directives.

2.29 To address all of the pollution risks associated with manures, slurries and grazing animals, it is essential to follow the guidance in "The 4 Point Plan", the individual components of which are:

  • minimising dirty water around the steading
  • better nutrient use
  • a risk assessment for manure and slurry
  • managing water margins

2.30 Guidance on "The 4 Point Plan" is available from the existing farm advisory network and copies are available free from SEERAD Area Offices (see Annex A).

2.31 Contractors or companies involved in spreading organic manure and slurry to land should be employed only if they are competent and suitably trained, are aware of their legal obligations and are willing to follow the guidance in this Code and adhere to "The 4 Point Plan". Always work closely with your contractor.

Air emissions

2.32 The saying "what goes up, must come down" is very appropriate in respect of livestock farming. Agriculture is the dominant source of ammonia emissions in the UK, mainly arising from the storage and application of manures and slurries. Ammonia emissions from livestock slurries and poultry manures, once re-deposited on land, can add excess N making soils more acidic. This can lead to "eutrophication" of water ("eutrophication" is described in the Nitrates Directive as "the enrichment of water by nitrogen compounds, causing an accelerated growth of algae and higher forms of plant life to produce an undesirable disturbance to the balance of organisms present in the water and to the quality of the water concerned"). Rainwater from poultry buildings that are ventilated to the roof should never be allowed to discharge directly to a watercourse (due to the deposition of dust, feed residues and animal/bird excreta).

2.33 Once emissions to air have been prevented, for example by covering a slurry store (if safe and practicable), it is essential that effective use is then made of the increased nutrient content of the slurry without increasing the risk to rivers and groundwater from application to land. Intensive pig and poultry installations exceeding the thresholds in the Pollution Prevention and Control (Scotland) Regulations 2000 as amended (the PPC Regulations) will require a permit from SEPA.

Treatment systems

2.34 Normally, the practices described in this section should be sufficient to prevent or at least minimise the risk of diffuse agricultural pollution. In some cases, however, it may be necessary to consider the installation of some form of treatment system near the source of potential pollution. It may be possible, for example, to install a wetland, pond or infiltration system to deal with contaminated roof or dirty yard run-off at the farm steading. Specialist advice should be sought on the selection, design and installation of such systems and SEPA must be consulted beforehand to ensure that the requirements of environmental and waste management legislation will be complied with. Treatment of non-agricultural waste to reduce the pathogens, or bacteria, present may be necessary to reduce the risk of microbiological contamination of nearby watercourses.

What can you do to prevent diffuse pollution?

2.35 The key to minimising diffuse pollution is to ensure effective control of the use and fate of potential pollutants. This can be achieved in a number of ways. Detailed advice on particular farming activities is provided in subsequent sections of this Code. Key measures include:

  • undertaking "good housekeeping" and waste minimisation practices that aim to prevent pollution at source
  • carefully planning all storage and handling arrangements for livestock slurries and manures, animal feedstuffs, silage effluent, agricultural fuel oil, dirty water, fertilisers, veterinary medicines, pesticides and other chemicals on your farm
  • distancing the potentially polluting farming activity from a watercourse by using a buffer strip (for example, a grass or woodland strip between the field and the watercourse)
  • if you are employing an agricultural contractor, make sure that they are suitably trained, qualified and competent to carry out the operation for which they are employed. Make sure that they are aware of the legal requirements, and are prepared to follow the guidance in this Code. Make sure that you provide the contractor with all the essential information specific to your site

2.36 Soil erosion on susceptible fields can be minimised by using minimum tillage systems, diversion systems and grass buffer strips, and also by adapting field activities according to local risks. Cultivated soils which are light textured should not be left without a crop or stubble cover during the autumn and winter period.

2.37 Where sedimentation ponds can be provided for run-off from problem fields, it is essential that accumulations of soil and settled particles are removed periodically and returned to the fields. Where sheet erosion is a problem, grass filter strips may be sufficient, and advice should be sought on suitable seed mixes to establish a strip and their subsequent maintenance.

2.38 Limiting the risk of diffuse pollution may involve the creation or use of field margins or other landscape features. These need to be carefully planned and may attract grant assistance on which SEERAD staff can advise. If a wetland treatment system is proposed professional advice should be sought and any potential discharge to a watercourse should be discussed with SEPA.

2.39 A buffer strip between field operations and watercourses is likely to reduce the risk of diffuse agricultural pollution but must also go hand in hand with other good management practices. Design of buffer strips will depend on local circumstances. The detailed design of a buffer strip will be closely related to the problem to be tackled, and specialist advice on the best way forward is recommended. A small margin is still going to be better than none.

2.40 The presence of field drains may allow diffuse pollutants to by-pass a buffer strip, and intercepting the drains might be the only way to achieve a significant reduction in risk. In certain cases, intercepting drains could result in the creation of wetlands or ponds. Such areas may attract grant assistance due to the provision of new habitat for wildlife.

2.41 A range of multi-agency guidance is available which will assist with the identification of diffuse pollution risks and the selection of Best Management Practices (BMPs) to address these risks.

2.42 Adhering to the good practices contained in this Code will help to prevent diffuse pollution from farming activities. The impacts associated with this form of pollution can be difficult to solve, however, and practical answers should be developed between farmers, SEERAD, SEPA, agricultural and conservation advisers. Often, the activities in a catchment area as a whole will need to be considered together and farmers should not hesitate to get involved in the increasing number of partnership initiatives being established throughout Scotland. By collectively doing a little to improve management, and to reduce risks, there is the potential to change a lot for the benefit of our environment.

Back to top