My (educated) guess (okay, theory) is that it is probably just one outcome of other related ecosystems problems, of course in addition to the over-fishing problem. For example, tying up freshwater streams for inland water human or livestock/crop use or polluting the ocean will also effect producer foodchain organisms, which in turn will effect larger and larger organisms. This could result in less larger organisms (fish). Couple that with over-fishing, it seems that the ocean is not all that re-newable of a resource.
Perhaps if humans ate on more of a producer level (more vegetables, grains, and fruits) the costs to the environment wouldn't be so costly? That, however, is more easily said than done...
