Speaking to reporters at Parliament today, Dr Smith said he was open to strengthening minimum standards for some rivers and streams. But cleaning up every waterway in New Zealand was an unachievable goal, he said.
"For instance we've got water bodies where there are large native bird populations where the bird poo makes the rivers unswimmable.
"The only legal way you could make these rivers swimmable would be to effectively cull that bird life."
Other rivers were polluted by volcanic ash or were polluted periodically by large weather events, he said, and it was impractical to require councils to ensure that they were able to be swum in all the time.
"What I am prepared to do is toughen up the rules on industry, on our urban areas, on our farming sector and on our councils to make sure that New Zealand lifts its game so that every Kiwi family can find a place that they can safely swim."
The minister is partway through a national roadshow on freshwater, which will help determine new "bottom lines" for freshwater and regulations for keeping livestock out of waterways.
As part of that process, councils will he required to identify waterways which are popular for swimming and were a high priority for protection.
Greeting the hikoi at Parliament today, party leaders from Labour, Greens and the Maori Party reiterated their pledge to make all rivers in New Zealand clean enough for swimming if in power.
Some of the hikoi made tearful pleas to the leaders that their younger generation were not left to "clean up the mess" in New Zealand's rivers and streams.
Addressing the crowd, Labour leader Andrew Little said he grew up in a New Zealand where most rivers could be swum in or drunk from.
"It's amazing to think that a couple of decades on, just how things have changed," he said.
The Ministry for the Environment's latest report card in 2013 showed that 61 per cent of monitored waterways were unsafe for swimming, compared with 52 per cent in 2012.