Which kind of worse is worse?
I am not a marine biochemist, but I would pick the metals as the worse of the two. They're likely to show up in the oysters and last until buried in enough clean sediment to cover them up. Assuming that the oyster dredges keep churning up the bottom, that top layer metal concentration could keep rising unless there's a type of vegetation that they could could use to chelate it. Grow the plants and harvest the metals.
The nutrient OTOH simply kills the marine life by suffocation, which is to say nothing of toxins released by the algae that feed on it (do you get a "red tide" there in the summer?). Then there are the bacteria.
However bad the nutrients might be, the system could eventuall purge them, so at least they aren't permanent.
Pick your poison.
So as bad as nutrients are, toxins and bacteria are worse? This makes me think that the nitrates might be less of a culprit and the toxins in the runoff might be the culprit. Not to mention a wildy swinging salinity range which seems to affect mitigation more than anything.
The water is pretty dark like a red tide but I don't think we have one. I'm going to start to take some measurements. Any suggestions on cheap instruments?