If your in San Diego the Birch Aquarium is decent. They have a 70,000 gallon kelp forest exhibit in the hall of fishes which exhibits from from the cold water pacific, tropical Mexico and the Caribbean, some 60 tanks total.
Not to mention the view is great overlooking the pacific ocean on the La Jolla bluffs.
The aquarium is part of Scripps Institution of Oceanography.
(Its my hometown aquarium.)
http://www.aquariumofthebay.com/ in San Francisco
Steinhart Aquarium (California Academy of Sciences) San Francisco
Monterey Bay Aquarium , Monterey Bay, California
http://www.cabrilloaq.org/index.html Los Angeles
Then of course if you enjoy theme park type aquariums or want to see marine mammals there is Sea World in San Diego.