Poor quality water could affect coastal waters many kilometres out to sea.
Freshwater ecologist Dr John Quinn gave the Whanganui River a pass mark for health, but said a lot more should be done.
The headwater diversions for power generation took out water from the hard rock volcanic area, leaving mainly water that flowed over soft rocks and collected silt, making it muddy. In summer, when most people swim, the water is usually clear enough for people to see their knees - but not the 1.4m to their feet, the bathing standard.
The Ohura catchment provided 24 per cent of silt in the river, and Dr Quinn wasn't sure silt quantity was decreasing, despite regional council efforts.
Bacteria levels were safe for fishing and swimming at all times, levels of nitrogen and phosphorous were low, and there were signs that insect life in the water was improving. Water temperature had risen slightly but significantly, which could be a consequence of climate change.
Alastair Bisley said the national Land and Water Forum he chaired went looking for solutions to the country's fight over freshwater. The result has been a national policy statement and objectives, and a recommendation to give iwi more say.
But journalist Rod Oram said the national policy statement was flawed, and the nitrogen levels it set were "ghastly" - lower than those set by two regional councils. The objectives should include measures of insect life, he said and predicted major legal battles over water quality.
Dr Jacinta Ruru said Maori wanted to keep human sewage out of water and many didn't want the waters of different catchments mixed - as happens in the Whanganui diversions.
Treaty settlements such as the one making the Whanganui River a legal entity offered more hope, she said.
Those on the trip up the river included 36 young people who were part of a McGuinness Institute workshop, charged with answering a question set by Treasury about the goals of regional New Zealand.
