Large parts of Cockburn Sound are not monitored because of a funding shortfall as research suggests the health of the fragile waterway is deteriorating, an environmental watchdog says.
Soon after a study found the Peel-Harvey estuary was under significant stress, the Cockburn Sound Management Council issued a stark reminder about major problems the southern harbour faced.
In its annual report, the council said in parts of the sound there had been "significant increases" in levels of chlorophyll-a - a green pigment which indicates algal growth - especially in the south.
It also noted there had been widespread and inexplicable reductions in seagrass cover - a key indicator of the waterway's condition - while there were elevated levels of heavy metals in other parts.
Some of the worst water quality recorded in the 12 months to June 30 was in Jervois Bay south of Coogee.
Mangles Bay in Rockingham had high nitrogen and phosphorus levels.
The report indicated the "seagrass picture is incomplete" near Garden Island because the Defence Department had been unable to monitor it, a source close to the council said, adding the episode was increasingly typical.
Although declining to be identified, the source said much of the monitoring that had previously been undertaken by businesses and agencies was no longer being done because of a lack of funding.
Hands Off Point Peron chairman Ron Chapman, whose group is fighting plans for a marina at Cape Peron in Mangles Bay, said the report highlighted how the area was already under environmental strain.
Dr Chapman said the proposed marina would make problems worse because it would inhibit seagrass growth, obstruct the sound's ability to flush and involve dredging contaminated soil.
Cedar Woods spokesman Stuart Duplock, whose group in partnership with LandCorp is behind the Mangles Bay proposal, acknowledged the CSMC report but noted WA's environmental watchdog had endorsed the marina.Mr Duplock said the project would not add nutrients to Mangles Bay nor have a material effect on seagrass health.