The Whanganui River's water quality is improving but Fish and Game warns it will never be pristine.
The latest recreational water quality report from the Ministry for the Environment shows most of New Zealanders' favourite monitored fresh water swimming spots are a health risk and should be avoided.
The ministry assessed 210 freshwater beaches and 248 coastal beaches used for recreation, based on monitoring data acquired during five consecutive summers.
The beaches were given one of five grades to describe their likely condition for recreation during summer, based on an assessment of potential sources of faecal contamination.
The Whanganui River was ranked "fair" and has gradually been getting better, Fish and Game regional manager Daren Smith said.
"Fair's okay, good would be better, very good would be ideal, pristine is something that we're never going to achieve," Mr Smith said.
Due to the hill country north of Wanganui, every time it rained farm run-off leached into rivers.
"Generally, all New Zealand rivers and waterways could be improved. There's no doubt about it," he said.
However, just because a river sometimes looked dirty did not necessarily mean that it was.
"Sometimes a dirty river is a healthy river. Sometimes it is just natural run-off where you see one stream feeding into another and we know for a fact that there's been a river further up," Mr Smith said.
Senior Massey University ecology lecturer Mike Joy said the report's results were not surprising.
The clear differences between the good and the bad sites were whether they were upland or lowland, he said.
"When I look at the local sites I know of - swimming holes like Horseshoe Bend on the Tokomaru River - it comes straight out of native forest and there's a lovely swimming hole and it's beautiful and, of course, there's no E.coli, there's no problem with bacteria.
"If you look at any of the sites downstream, they fail because of all of the run-off from dairy farms and the effluent from the wastewater treatment plants," Dr Joy said.
The report highlighted the effects of uncontrolled intensification of dairy farming and a complete failure of protections on fresh water, Dr Joy said.
Stronger legislation, fencing waterways off from cattle and riparian planting was needed to help protect fresh water from further contamination, he said. APNZ
Best and worst
Very good: Lake Dudding and Lake Wiritoa
Poor: Kaikokopu Stream at Himitangi Beach, Mowhanau Stream at Kai iwi Beach and Wairarawa Stream at Waiterere Beach
No rivers that ranked "very poor" in the Manawatu-Wanganui region
Clean green?
Of the 458 monitored beaches that were graded:
17 per cent of freshwater beaches and 18 per cent of coastal beaches were "very good"
A further 15 per cent of freshwater and 42 per cent of coastal beaches were "good"
24 per cent of freshwater beaches and 25 per cent of coastal beaches were "fair"
24 per cent of freshwater and 13 per cent of coastal beaches were "poor"
21 per cent of recreational freshwater beaches and 3 per cent of coastal beaches used for recreation were "very poor"