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Find an organism that passes through the passage and a way to track that.

Hitch your wagon to something living that will be able to find a way.

A fish with a GPS tracker perhaps? If they attach them to ground animals, why not water?

They also/already attach them to whales, sharks and dolphins, at the least. I bet someone, somewhere, have done it to a fish...

The limit is probably the size of the tracker. The ones I saw look about as big as a standard river fish..

Try otters. They'll eat the zebra mussels when they're done.