The watchdog that manages the Swan and Canning rivers has reported a surge in illegal activity and has complained about damage to the waterways by careless users.
A Murdoch University study has suggested there are signs of life recovering in the waterways but a separate Swan River Trust report says various damaging practices are affecting its health.
The trust report comes amid much-criticised moves by the Barnett Government to axe the trust and roll it into the Department of Parks and Wildlife as part of efforts to cut red and green tape.
Tabling its latest annual report, the trust noted that in the year to June 30, the number of unauthorised developments along the rivers' banks jumped to a record 46 from 13 the previous year.
It is believed many of the offences related to illegal dams in the upper catchments of the Canning and Helena rivers.
Land users also built structures such as pontoons and barbecue areas without permission.
The number of known industrial discharges and illegal dewatering from the rivers rose from 11 to 19 in the year and there was a sharp rise in reported "aquatic deaths", including mass fish deaths.
In a series of incidents during the longest algal bloom recorded in the Swan - between May and December last year - about 14,000 fish died when levels of a toxic form of algae spiked.
However, the trust was especially critical of people who chopped down or pared back protected trees to improve their views, saying it remained a serious issue.
The increasing reach and levels of salt water upstream was also "taking its toll" on the agency's oxygenation plants, meaning they had to be run longer and were damaged more than forecast.
The Murdoch researchers found fish populations in many parts of the Swan and Canning rivers were relatively healthy and appeared to reflect the system's improving health.
"Given the publicity around the supposedly poor state of the estuary in recent years, the results were perhaps a little surprising," senior researcher Chris Hallet said.