Tidal flow in an estuary
The tidal flow velocity is not the same thing as the mass movement. Think of the tidal flow as a pressure pulse that moves up the river. It moves much farther than the actual salt water movement. The extent of the brackish zone is much shorter. The relationship depends on the river flow and the shape of the estuary.

In your case, your source area is within the limit of saline intrusion so there is some mass movement upstream. Given that you are studying bacteria particles rather than dissolved salt, I would say that the limit of saline intrusion marked on your map is an upper limit for the distance it could move upstream. That is assuming that the bacteria haven't established a stable population that can reproduce and grow outward.