Fishing methodology has a lot to do with it. Bottom trawling can "reel in" many species that should have stayed in the water. Globally, fishing fleets are much larger than is necessary to take in fish and other species, particularly as to what the oceans can sustainably support. Consider this... according to the group overfishing.org, globally the fishing fleet is large enough to cover four Earth-like planets!
According to one source on the NBC news program on the subject, 90% of the large fish are gone. The most serious of these is one of the world's favorites, the bluefin tuna. 52% of the world's fish stocks are fully exploited, says overfishing.org - they are at their maximum sustainable production level. 17% are over exploited, with 7% depleted.
What can we do? Education about the issue is the first step.
Refrain from eating those fish you know to be in danger. The Monterey Bay Aquarium has a good guide on the subject, here.
Contact your governmental representatives and talk up the issue. Remember to mention that habitat protection is one of the keys, and that fishermen and fleets need to be monitored -- fine those who violate the laws, making it uneconomic to cheat.
Tell your friends. Ask them to jump onboard.
I'd like to think I will still be able to eat tuna 20 years from now. Wouldn't you?
