Reading on the topic:
http://www.utsandiego.com/news/2011/...-from-several/
http://www.utsandiego.com/news/2012/...s-sd-bay-fish/
http://www.utsandiego.com/news/2012/...us-amounts-of/
http://www.waterboards.ca.gov/water_...2012report.pdf
http://www.waterboards.ca.gov/rwqcb9...arch.30.05.pdf (See the back of the report)
Basic take away: I would be hesitant to eat much fish from San Diego Bay, but Mission Bay, for the most part seems not to have elevated levels of PCB and levels of mercury that aren't higher than other CA coastal waters. Shark seems to be particularly high in mercury in a number of studies, so I would limit consumption of shark.
BTW, the Environmental Health Coalition is one organization that is working on getting SD Bay cleaned up:
http://www.environmentalhealth.org/i.../san-diego-bay
Another is SD Coastkeeper:
http://www.sdcoastkeeper.org/learn/r.../sediment.html