A government report shows many regions are a long way from achieving water quality standards set by the previous government, which were criticised for being too lax.
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The joint report by regional councils and the Ministry for the Environment and the Ministry for Primary Industries reveals Northland and Auckland have the dirtiest rivers, with fewer than one in four clean enough for swimming.
Under the standard set by the previous government, 90 percent of larger rivers and lakes must be swimmable by 2040.
Ministry for the Environment deputy secretary Cheryl Barnes said improving water quality was complex.
"Having some standards in place is a useful step always, it's tricky to work out what the right standards should be, so you know there'll always be some debate about that and as we get new and better information that always helps us refine that over time."
Ms Barnes said the report would help communities understand where more needed to be done.
Massey University ecologist Mike Joy said the goal that 90 percent of larger rivers and lakes must be swimmable ignored smaller rivers, which account for 90 percent of waterways.
"To take such a stupid target such as 90 percent of 10 percent of our waterways and then make it off in the distance some time to have to achieve it is just wasting everybody's time, I think if the money spent on doing these reports was actually spent on doing something about it, we might actually get somewhere."
The government had a mandate from the electorate to improve water quality and it was time to stop giving farmers special treatment and make them pay their way, Dr Joy said.
But a farming lobby group is warning tougher requirements for fencing waterways would drive some out of business.
Councils have already committed to $217 million a year worth of improvements in cleaning up waterways, of which $135m will be borne by the rural sector.
Federated Farmers water spokesman Chris Allen said this cost didn't include fencing off sheep from streams, which would increase the cost ten-fold.
"It's probably the quickest way we could make everyone go bankrupt is go beyond what is deemed to be reasonable when it comes to fencing."
Mr Allen said farmers were already doing a huge amount of work to clean up waterways but the costs had to be proportionate to the benefit.
Auckland Council said it had got public support for a plan to charge households a targeted water quality rate to clean up polluted rivers and beaches.
Auckland Council's water strategy manager Andrew Chin said many popular beaches were also contaminated with E Coli.
"We do have a plan, we want to bring that investment forward, we've gone to Aucklanders over the last month ... and there's been a fairly substantial positive feedback on the proposal to pay for the targeted rate to address these water quality issues faster."
Mr Chin said the targeted water rate in Auckland's draft 10 year budget will help cover the $2 billion cost of upgrading wastewater and stormwater networks.