Agriculture in general has two main potential negative impacts on surface water and groundwater:
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Diffuse pollution caused by sediments, nutrients and pesticides entering waterbodies, including the sea and groundwater.
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Physical damage to wetland habitats (stream channelisation, loss of woody debris, wetland drainage, infilling of ponds, alteration of hydrology).
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| The general impacts of agriculture on the quality of freshwater ecosystems are clear, and can be easily demonstrated by comparison with streams and ponds in uncultivated catchment areas. Typically, freshwaters in agricultural areas support a smaller proportion of sensitive plants and animals. Streams and rivers in agricultural catchments usually remain in good condition until about 30-50% of the area is cultivated. The proportion may be smaller for lakes and ponds, which have a lower capacity for dilution of pollutants. |
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| The effect of diffuse agricultural pollutants on freshwaters |
| There are three principal types of agricultural pollutant: sediment, nutrients (both natural and synthetic fertilisers) and pesticides (natural and synthetic). At present the main known impacts of these different diffuse pollutants are: |
- Sediments: Soil particles can transport nutrients, particularly bound phosphorus, and alter stream-bed habitats by smothering coarser substrates with fine particles.
- Nutrients: Nitrogen, phosphorous and other nutrients enter water bodies either as dissolved or particle borne materials, cause major changes in standing water ecosystems, typically by promoting the growth of algae at the expense of large water plants. Effects also occur in running waters but are less well understood.
- Pesticides: A variety of pesticides may enter water by spray drift, water runoff from fields or bound to soil particles. They may have impacts on all biotic groups, the nature of which will depend on the type of pesticide, level of exposure and sensitivity of the biota. Modern pesticides are tightly regulated and the relative contribution to the overall degradation of water courses by agriculture is poorly understood, but is generally thought to be relatively small.
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 In many freshwaters the addition of polluted silty water often means that few submerged plants survive and only robust and tolerant invertebrate animals remain. In streams and rivers, deposition of silt on bottom sands and gravels can often also reduce the availability of egg-laying sites for fish particularly for rheophilic species such as chub, dace and gudgeon.
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| Overall, it is difficult to determine which of the three main diffuse pollution sources associated with agriculture has most impact on aquatic ecosystems; indeed it is often impossible to separate these effects because all tend to occur together, particularly in arable landscapes. |
The hope is that by reducing the sediment load in run-off water, ponds and watercourses will have: |
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Clearer water
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Fewer pollutants
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More varied bottom sediments
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| and as a result freshwater biodiversity will benefit. |
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| Diatoms, an indicator species |
| Diatoms, single-celled (mostly) algae, are sensitive towards environmental stressors such as eutrophication, organic discharges, metals, toxic substances, unusual flow events, scouring and grazing. In Europe and the USA diatoms are now widely used in routine monitoring of water quality in streams and rivers. |
 Compared to other biological indicators diatoms have several advantages. They are found in almost every habitat and are easily spread in and between river systems. As primary producers they play an important and fundamental role in nutrient cycling, food webs and oxygenation of surface waters. Short generation time enables them to respond directly and rapidly to ecological changes. |
| Buffer-strip ponds |
| In theory, buffer strip pools have the potential to reduce pollutant levels in field drainage by providing opportunities for sedimentation, de-nitrification and nutrient uptake by algae and macrophytes. Similar pond treatment sequences are now widely used to ameliorate urban runoff, and treat some industrial effluents. However the approach has been relatively little applied or tested on farmland. The potential multi-functional value of these features in terms of the new freshwater habitats they provide has been little evaluated in any environment, although recent evidence suggest that the creation of new ponds may bring considerable biodiversity benefits. |
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| Series of ponds receiving water from broken fields drains |
