Record numbers of salmon and sea trout were found in the Mersey, Tyne and Thames, while otters returned to every region in England and Wales.
The decade also saw the return of the water vole after a dramatic decline in the 1990s.
Incidents of serious water pollution have more than halved since 2001.
The River Thames won the International Theiss River Prize for outstanding achievement in river management and restoration earlier this year.
Ian Barker, head of water at the Environment Agency, said: "The last decade shows how far we've come in reducing pollution and improving water quality and river habitats.
"Rivers in England and Wales are at their healthiest for over a century, with otters, salmon and other wildlife returning to many rivers in record numbers in locations across the country." Read the full report here.
Source: BBC News, UK.