Emergency services were called to Mandurah estuary about 10pm on Saturday after a boat with four people on board struck a red post marker.
A 54-year-old woman was recovered from the water but could not be revived and died at the scene.
A 47-year-old man, believed to be the boat's driver, was taken to hospital with serious injuries, while a 54-year-old man was uninjured.
Emergency services are searching for a 52-year-old woman who remains unaccounted for after she went overboard in the crash.
Assistant Superintendent Peter Morrissey pointed to his experience in other searches and the time since the missing woman had last been seen.
"We're probably in a space where we're looking to recover the body," he said.
Police earlier reported the woman's body had been recovered but have now advised that was an error, with an accidental report logged after searchers found property belonging to the missing woman.
The deceased woman and the missing woman's next of kin had been contacted, police said.
Investigators will consider speed as a factor in the crash.
"It's way too early at this stage to determine any sort of criminality," Assistant Supt Morrissey said.
He said the estuary was busy on Saturday so there were a significant number of witnesses to interview.
Parts of the estuary were closed off as police investigated the crash site and surrounds and emergency services continued the search for the missing woman.
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