Most rivers, lakes and other waterways in England and Wales are unlikely to meet EU regulations on water conditions, conservationists say.
The EU directive does not come into force until 2015
The Royal Society for the Protection of Birds says much work needs to be done to meet the EU targets set out in the Water Framework Directive.
It based its comments on water status reports from the Environment Agency.
The rules do not need to be met until 2015 but there is concern about a lack of investment to meet the targets.
The conservation group said there would be the threat of heavy financial penalties if the UK failed to comply.
But RSPB water policy officer Sarah Oppenheimer said rather than facing fines, meeting the directive's targets could save money by reducing the need for clean-up operations.
"Every year customers are paying millions of pounds to remove farm chemicals from drinking water. Instead we should be preventing pollution in the first place," she said.
"We must also manage our land and rivers better to reduce the risk of floods. The Water Framework Directive will tackle all these problems."
Environmental groups, such as the RSPB, said in the past very limited parameters have been used to measure the quality of UK waters, mainly looking at chemical concentrations.
However, the water framework directive has a much wider scope looking at, for example, how much water is being taken out of waterways and whether fish have places to spawn.
The directive is intended to improve waterways and wetlands, ensure water is used in a sustainable way, to reduce water pollution and to lessen the effects of floods and droughts.
EU members must submit an appraisal of the condition of its waterways by March next year, with directive targets needing to be achieved by December 2015.