My biggest concern is that along with the nitrogen and phosphate runoff come pesticides and other less savory compounds that then bio-accumulate in the farmed shellfish.
It depends on whether or not they bioaccumulate^W -- checking wikipedia apparently the word I want is biomagnification.
The basic idea is that as you move up the food chain the concentration of toxins gets higher. So a plant might have a relatively low level of toxin absorbed even if it was directly applied, but a shellfish that consumed algae that were exposed to the toxin downstream from the farm might have a considerably higher level.
I don't know a whole lot about the details in this specific case, but that's my concern.
