I was always told as a kid that fishing the river after a heavy rain affected the fish. How much it had to do with the salinity of the water...I don't know. I think it had more to do with the water color and drop in temperature over the salt content. However, I have heard a wide range of fishermen say that they look for "saltier" spots to fish for saltwater species
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I think this may hold somewhat true. Especially, after they leave to spawn. Younger flounder must be able to withstand lower salinity water, since they will live in the rivers and bays for a couple of years before going into the ocean. The lower salinity of the water does possibly slow their growth rate and they will pick spots with higher salt, however, they are more picky about what is on the bottom. They will stay somewhere with lower salinity that has a better sandy bottom over a non sandy bottom with higher salinity.
This does make sense, since most bigger fluke are caught in the saltier ocean on sandy areas.
So, from my understanding and to answer your question, yes the fluke will move to saltier areas after a heavy rain, especially the larger ones. Tide will of course bring in more salt content and the difference you will see will probably be minimal. There are a lot of factors that will affect this.
Maybe someone who has studied Marine Biology or has some background education in this can give a better answer...fishin4life
On a side note...heavy rains and freshwater will make the crabs grow bigger as they prefer lower salinity and grow bigger in less saltier water
. Yummmm!