The dead whale is at least 36 feet long and was found floating in the Oakland Estuary.
PHOTOS: Dead whale found under doc in Alameda
The U.S. Coast Guard notified the fisheries service of a stranded whale floating in the waters between Alameda and Oakland at about 4:30 a.m., according to Justin Viezbicke, the fisheries service's California stranding network coordinator.
The whale has washed in and wedged into the pilings at Berth 46 in Alameda.
Researchers arrived Wednesday afternoon to take tissue and blood samples to determine what kind of whale it is. Right now, it is hard to tell because its head remains submerged.
They are looking at options to pull the whale from the water for study, but such an operation would be expensive and difficult.
The people who run the yacht business above these docks say they have called the coast guard and several agencies about removing the carcass. "Who knows how long it will be here. We don't what it to be a distraction for boats or a hazard to navigation. That is our concern," Christina Wright said.
The Marine Mammal Center told ABC7 News the National Oceanic and Atmospheric Administration is involved along with the U.S. Coast Guard.
It is unclear at this time how or when the dead whale will removed.
The dead whale is the latest of several that have turned up in the Bay Area, including three found on the shores of Pacifica since April. However, it is the first reported in the Bay itself this year.
Bay City News contributed to this story.