Officials say that during the cleanup, police officers responded to a report that a woman was kept in a tunnel near the beach against her will.
Officials say the woman was not there but found the checkbook and driving license of Colby Storey, 32, who has been missing since December.
Officials then searched the nearby Balona Wetlands Ecological Reserve and the Balona Creek area and found skeletal remains.
Those remains have been processed and sent to the Los Angeles County Coroner for formal identification. The LAPD has not confirmed to whom the remains belonged.
The woman’s family and friends were involved in the search, along with police officers on horseback, and K-9 units from the California Emergency Services Office.
Meanwhile, the authorities sanitized the homeless camps with the city’s sanitation workers removing the abandoned items.
Los Angeles City Councilman Mike Bonin, who represents the area and could face a recall campaign, said 188 people had been moved from the Venice boardwalk to shelters.
Mr Bonin launched a “Camp for Home” program in June, designed to clear the historic boardwalk of temporary shelters.
The LA City Council is spending $5 million on the project, which provides temporary housing at motels before participants move into permanent housing.
Last month, LA County Sheriff Alex Villanueva sent a deputation to Venice Beach to evacuate some homeless people from the area, despite no jurisdiction.
Earlier this month the LA City Council approved an ordinance that would ban homeless camps from sidewalks and several other parts of the city.
According to federal figures, California is now home to more than a quarter of the nation’s homeless population.