If you prefer to catch marine life with your camera rather than a hook and line, consider taking a whale-watching cruise out from the San Diego [1] coastline. Most of the sportfishing outfits [2] also offer whale-watching trips and charters in season (winter through mid-spring).
Hornblower Cruises (1066 N. Harbor Dr., 619/686-8700, www.hornblower.com [3]) offers daily nature cruises at 9:30 a.m. and 1:30 p.m. year-round. This nearly four-hour adventure is great for families, and includes a kid-friendly marine habitat video; seal, sea lion, and dolphin viewing; and guaranteed whale spotting.
Hornblower offers one of the most comfortable, tourist-friendly sea experiences, with a snack bar, indoor decks with panel windows for good viewing, and a yacht highly rated for its stability.
Links:
[1] http://www.moon.com/destinations/california/san-diego
[2] http://www.moon.com/destinations/california/san-diego/sports-and-recreation/fishing
[3] http://www.hornblower.com