Yet McDowell and his colleagues found it was these very bodies that accounted for an average of 77 per cent of the national contaminant load, varying from 73 per cent of total nitrogen to 84 per cent for dissolved reactive phosphorus.
"This means that to substantially reduce contaminant losses, other mitigations should be investigated in small streams, particularly where fencing of larger streams has low efficacy," the authors reported.
The Ministry for the Environment's Our Freshwater 2017 report indicated that urban waterways had the worst overall water quality in New Zealand, but much of the public focus in recent years had been on the impact of agriculture - particularly dairy farming - on waterways in rural areas.
"Fencing is very effective at reducing contaminant loads to waterways - by 10 to 90 per cent depending on the nature of the contaminants and local issues," McDowell said.
"Fencing works especially well for the likes of E.coli or phosphorus contamination that can result from animal waste or stream bank destabilisation."
However, fencing all waterways in New Zealand was "impractical" and in some places other good management practices may be more cost-effective, he said.
"A combination of better awareness of the issues and the use of good management practices - including fencing - in the right place is starting to reverse degrading trends in the likes of phosphorus and sediment in the water over the last decade."
Dairy farmers had invested in a major programme of fencing waterways to the equivalent of nearly 27,000km.
They should continue to do so as it was effective at reducing waterway contamination, he said.
"The fact that most of the contaminant load comes from areas not requiring fencing reflects the much greater number and areas occupied by small streams - potentially from steeper country where dairy farming is unlikely to be present.
"Other work also indicates that a substantial proportion of contaminant concentrations may be from natural sources."
Fish and Game chief executive Bryce Johnson called the study an "extremely important piece of research".
"We now have the science to show what we have long suspected - small waterways are crucially important to the environment and need to be properly protected from contamination."
Johnson said the research also called into question the dairy industry's claim that it was fencing 90 per cent of the country's waterways.
"The dairy industry is only talking about 90 per cent of larger waterways which have to be fenced anyway - not the critically important smaller ones where most of the pollution is occurring," he said.
"These smaller streams are vital to the environment - they flow into the bigger streams and rivers and Dr McDowell's research shows that by the time they join up with bigger streams, much of the pollution has already occurred.
"If the farming sector is serious about reducing its impact on water quality and restoring rivers to be swimmable, then it has to exclude stock from all water bodies - regardless of size - and create more extensive riparian buffer zones."
The National-led Government had been finalising details on national stock exclusion regulations.
But most dairy cattle and pigs had been required to be fenced off from waterways since July, with a goal to extend this to all stock by 2030.
Its definition of waterways subject to the rules were "permanently flowing waterways and drains greater than one metre wide and 30 centimetres deep", but also smaller ones on the plains, where landowners would have until 2020 to comply.
The regulations also applied to "natural wetlands", but not including damp gully heads or places where water temporarily ponded, or built structures, such as effluent ponds, reservoirs or channels.
The research was funded through the Our Land and Water - Toitu te Whenua National Science Challenge, of which McDowell is the chief scientist, and published in the international Journal of Environmental Quality.
