The mussels and clams do filter stuff out of dirty water. However the stuff they filter out is food for them which they digest and chemically convert into stuff like more mussel and clam tissue. That is how organisms grow, they are what they eat.
Now if there are persistent toxins in the water that the mussels cannot break down and can build up in them then sure, they wouldn’t be healthy to consume. Heavy metals for example. But water dirty from something like human or animal waste is something they can biologically process.
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