Look up the Chesapeake Bay and crab fishing. The worst pollutant has actually been silt - unfiltered soil from shoreline housing projects spills into tributaries and flows into the bay, and has been a major contributor to a serious drop in Oxygen levels in the bay, which has caused fish kills and reduced the already over-fished blue crab population. Chemical pollution is also a problem, mostly through mercury vectors. Mercury is a man-made pollutant, and is magnified in amount as traces move up the food chain. People in the US and other countries have been warned away from the consumption of certain fish because of high mercury levels. I'm sure a short google search will lead you to more specific examples.
*edit* I forgot to mention farm runoff: fertilizers can cause toxic algae blooms in local fisheries.
