A study by the World Wide Fund for Nature conservation group found that 50 out of 69 river stretches in 16 European countries suffered from "poor ecological status."
The group said on Friday that the EU needed to do more to meet its own environmental standards.
The ongoing water study, which will investigate most of Europes rivers, is being carried out over a two-year period which started in April 2000.
It found that rivers in some European countries still outside the 15-nation EU had waterways cleaner than those in the EU.
The WWF said the Rhone and Seine in France, the Ebro and Segura in Spain, the Severn in Britain, the Danube in Austria, the Maas and Scheldt in Belgium were among the worst polluted rivers in Europe.
They will all require major restoration works and other actions to meet "good ecological status" before the end of 2015, as required by the EU Water Framework Directive, the WWF study found.
"Although heavy pollution in Europes rivers is reduced, most European rivers are far from achieving their ecological potential," head of WWFs European Freshwater Programme Jane Madgwick said on Friday.
Of the rivers examined by WWF only a handful already meet future the requirements of the Directive, including the Wye and the Usk in Wales, the Teno in Finland, the Morava in Austria, the Coe in Scotland, the Derwent in England and the Semois in Belgium.
The study blamed the poor state of the waterways on continuing damming and canalisation.
It also said European industries continue to dump waste into rivers, while the run-off of agricultural fertilizers is also seeping into rivers.
The WWF called on European nations to enact the stringent new EU environmental rules which aim to clean up and restore rivers, marshlands and lakes to their original ecological state by 2015.
"European heads of government have signed up for a big improvement in Europes rivers," Madgwick said.
"It will require a substantial investment but the costs of reviving Europes rivers will be more than repaid by long-term savings in flood damage, water treatment and public health. WWF will be keeping a close eye on EU countries to make sure they live up to these commitments."
Rivers of Shame
Rivers of Praise