Eutrophication conditions in Lough Neagh were originally thought to be due to high inputs of phosphorous from point sources, mainly waste-water treatment works (WWTWs). However reducing the phosphorous discharged from the ten major WWTWs in the Lough Neagh catchment, which commenced in the early 1980s, only lowered the lake concentration until 1987. Since then there has been a steady rise in the total phosphorus concentration of the Lough. This increase is primarily due to increasing river loadings of soluble phosphate.

It is likely that therefore that the dramatic enrichment of Lough Neagh, which occurred in the 20th Century, had been the result of increased nutrients coming both from urban and agricultural sources. While the urban sources have been reduced since 1981 and the phosphorous content of detergents had decreased appreciably since 1986, the agricultural inputs to Lough Neagh have continued to increase.

As well as levels of nutrients within the water column of the Lough and rivers there has been a considerable build up of nutrients in sediments that may slow down any recovery of the system due to nutrient release and recycling. It is thought that the large population of Lough Neagh flies may be a result of the Hypertrophic condition of the Lough.

Pollution incidents are specific events that result in the release of an undesirable substance to a watercourse or underground stratum. These substances may come from farm, domestic and industrial environments. They may include slurry, silage effluent, pesticides, herbicides, fungicides, detergents, sewage, hydrocarbon oils, and heavy metals. Their influence vary and involve short and long term consequences and localised and widespread effects. They can pose severe threats to the environment and to human health. Early detection is essential in reducing their influence. Some pollution incidents can be deliberate, others can be as a result of an accident.

The quality of water can also be based on its bacterial content related to particular uses. All water contains various types and numerous amounts of bacteria, most of which are harmless to humans. However, some bacteria when ingested or absorbed can cause illness. At present it is a statutory requirement that water extracted for human consumption by Water Service is tested and treated to ensure it meets acceptable standards. The statutory agencies do not test for bacterial content in relation to water sports, but in some in-shore areas of the Lough, local authorities carry out their own testing and they have prohibited contact water sports because of levels of illness-causing bacteria.