Farmers are being blamed for an increase in harmful nutrients in our rivers.
A 20-year study by Niwa found waterways flowing through farmland have higher levels of nitrogen and phosphorous than those that flow through unfarmed land.
Excess nutrients can increase plant and algal growth and, in extreme circumstances, cause toxic algal blooms.
Such problems affect recreational use of rivers, such as fishing and swimming and their aesthetic and ecological values. They can also harm lakes and coastal environments.
New Zealand has about 425,000km of rivers and streams.
The survey, for the Environment Ministry, saw Niwa staff collect more than 18,000 water samples from 77 sites on 35 of our largest rivers between 1989 and 2007.
The samples were usually taken on the same day every month, placed in an insulated container under crushed ice and freighted to Niwa's Hamilton laboratory for analysis.
Nitrogen levels rose at 52 sites and fell at none. Phosphorous levels increased at 22 sites and fell at only nine.
The ministry said the increase in nitrogen signalled a long-term trend towards conditions "likely to trigger undesirable changes to river ecosystems".
Niwa's principal scientist Rob Davies-Colley said the increases were greater in areas of farmland where waterways could be contaminated by fertiliser run-off.
"It's farm use of land that is driving our water quality in the wrong direction.
"At some point the water is not going to be sustainable for use, so we need to reverse that trend."
Federated Farmers' dairy chairman Lachlan McKenzie said members were aware of their impact on the environment but deserved credit for the environmental improvements they have made. They used much of their animal waste as liquid fertiliser and 78 per cent of dairy farmers had fencing around waterways under Fonterra's clean-streams programme. He said New Zealand's 1200 dairy farmers accounted for a quarter of total exports and were targeted as an "economic tall poppy".
"Farmers genuinely care about what they do and what impact they have."
But Fish and Game New Zealand spokesman Rick Cullinane accused Federated Farmers of not wanting to take any responsibility for the problem.
"We keep pushing our clean and green image but the reality is getting worse and worse. The effect on the fishery means that the water quality is poor and there's less fish."
Justine Daw, manager for the ministry's environmental reporting programme, said the survey results could be used as an early warning system for local authorities responsible for managing rivers in their areas.