White sharks around California prefer cooler coastal waters that extend out to the open ocean. San Francisco Bay is also a very murky environment where visibility (how far you can see through the water) may play a factor as to why white sharks are not around the Bay as much. Great whites have been found to rely upon eye-sight for much of their hunting strategies, particularly when it comes to catching some of their favorite foods – seals and sealions. Finally, the amount of prey (i.e. seals and sealions) that are accessible and easy for white sharks to catch are less common in the bay. White sharks develop very unique strategies for hunting their prey where it is most abundant in order to increase their odds of a meal. Even though there are plenty of sealions at Pier 39, San Francisco Bay is not the most suitable environment for white sharks to catch them.

With all of that said, there is a decent sized population of white sharks that spend a good portion of the year just outside of San Francisco Bay along the coast. I wouldn't be surprised if one or two didn't occassionally venture into the Bay beyond the Golden Gate Bridge to have a quick look around.