Conservationists fear industrial polluters are getting away with dumping waste into drains emptying into the Swan and Canning rivers because of a lack of environmental policing.
An environmental audit program to stop businesses pouring contaminants into drains was axed last year and a community-driven monitoring program had its funding cut.
Not-for-profit landcare group SERCUL chief executive Julie Roberts said the effect of cutting the programs was that polluters were being given free rein to dump whatever they liked into rivers.
Research has found that fish in the river at Claisebrook Cove in East Perth are showing signs of excessive exposure to contaminants and are changing their sex in response to the pollution.
Ms Roberts said no government agency was monitoring what contaminants were entering the rivers regularly, leaving the system vulnerable to pollution from toxic pesticides, heavy metals and other contaminants.
SERCUL had been monitoring contaminants but funding for that program was coming to an end.
Friends of Lightning Swamp president John Williams said the group feared the Noranda wetland, an A-class reserve fed by drains from the Malaga industrial area and which drains into the Swan River, would be destroyed by contaminants.
The audit program picked up high rates of non-compliance among businesses in the light industrial area in the way they handled, contained and disposed of waste near and in the drains and monitoring found high levels of heavy metals in stormwater discharging into the reserve.
The contamination of the reserve reached such a high level a few years ago that residents have been warned not to let their dogs play in the toxic water.
Lightning Swamp is home to at least eight species of frog, half of them threatened. A Swan River Trust spokeswoman said an investigation of contaminants in sediments throughout the estuary and drains entering the Swan and Canning rivers was done in 2009 and the results would be available this year.
Environment Minister Bill Marmion said water quality monitoring was done throughout the Swan- Canning river system.