Post-war changes in farming systems and especially the move from mixed arable-livestock farming towards greater specialisation, together with the general intensification of food production have had adverse affects on the environment. Livestock systems have largely become separated into pasture-based (cattle and sheep) and indoor systems (pigs and poultry). This paper reviews water quality issues in livestock farming areas of the UK. The increased losses of nutrients, farm effluents (particularly livestock wastes), pesticides such as sheep-dipping chemicals, bacterial and protozoan contamination of soil and water are some of the main concerns regarding water quality degradation. There has been a general uncoupling of nutrient cycles, and problems relating to nutrient loss are either short-term direct losses or long-term, related to accumulated nutrient surpluses. Results from several field studies indicate that a rational use of manure and mineral fertilisers can help reduce the pollution problems arising from livestock farming practices. Several best management practices are suggested for the control of nutrient loss and minimising release of pathogen and sheep-dip chemicals into agricultural runoff.