The Green Party says tougher policy is needed to improve water quality.
New data collated by the Environment Ministry from regional and district councils on freshwater and coastal spots shows more than half of the monitored rivers are of poor or very poor quality because of the risk of illness from e.coli.
The Greens' environment spokesperson, Eugenie Sage, says the current policy is too weak. She says catchments, particularly lowland spots, are being affected by agricultural intensification and poor sewage treatment.
Ministry spokesperson Guy Beatson told Nine to Noon that regional councils are now required to set limits on the amount of nutrients, e.coli and other bacteria in individual catchments by 2014.
He says the Land and Water Forum will also soon be reporting back to the Government with further recommendations on water quality.
The report found most beaches are safe for swimmers.