The council would monitor levels of the harmful bacteria but Mr Burton said the water should clear naturally. An E. coli risk of "secondary contact" with rivers - such as wading or boating - only affected 2 per cent of all New Zealand sites.
Study co-author and Niwa water-quality scientist Graham McBride said of those sites that could be compared, more appeared to be improving than deteriorating. Of 396 regional council sites monitored between 2004 and 2013, 54 had increasing concentrations and 81 had decreasing concentration.
A trend could not be determined for 261 sites.
Mr McBride believed keeping cattle out of streams by fencing off waterways would have brought benefits in rural areas.
The dairy sector has reportedly spent more than $1 billion on measures to protect waterways, and from May will be subject to requirements under its Water Accord, prohibiting all stock from any permanently flowing rivers, streams, drains and springs more than 1m wide and 30cm deep. According to Dairy NZ, more than 96 per cent of waterways on dairy farms now excluded dairy cattle.
"On the other hand, however, we've now got more of some animals than we used to have, which means there is more being deposited on the land," Mr McBride said.
While E. coli levels could spike during high rainfall events - when faecal material was washed off land - high concentrations could also be caused by animals defecating directly into low-flowing rivers.
People could check the state of their local river at the Land Air Water Aotearoa website.
Additional reporting Jamie Morton