Police got a call at about 7:30 a.m. from a man who had pulled over near Potter Street to talk on the phone and noticed a car in the water, Berkeley police Sgt. Mary Kusmiss said.
The vehicle, a blue 1995 Nissan Maxima, was mostly submerged about 15 to 20 feet from shore at the south end of the park near the on-ramp to eastbound Interstate Highway 80, she said.
Police and firefighters responded, and officers spoke with a second person who had been sitting in a car parked nearby for half an hour and hadn't noticed anything suspicious.
The first concern was that there was someone inside the Nissan, but firefighters extended their ladder over the water and were able to confirm that the passenger compartment was empty.
Crews then accessed the trunk to make sure there wasn't anyone inside. Meanwhile, police searched the area and didn't find anything else suspicious.
Investigators learned that the car had recently been stolen from San Francisco's Potrero Hill neighborhood. The owner didn't know until this morning that it was missing, Kusmiss said.
The car was removed from the water and taken to the Police Department's tow yard to be examined.
Police are now contacting neighboring agencies to see if the vehicle might have been used in a crime in the area.
Kusmiss said it is not uncommon for stolen cars to be dumped at Aquatic Park, which is dark and deserted at night, but that cars aren't usually found in the water.