The biggest reason why the Ft. Myers area (actually Ft. Myers down past Goodland and to Chokoloskee Bay) is so polluted is because the Lake Okeechobee Agricultural Area drains into the Caloosahatchee River and numerous man-made canals south of the Caloosahatchee. This agribusiness fertilizer runoff combines with the stormwater runoff, and deposits all kinds of nasty sediment on the bottom.
Several more man-made canals also afflict the east coast
of Florida, in particular the Indian River Lagoon
area. There is a marvelous woman who used to be mayor of Sewall's Point in the IR Lagoon
who has a tremendously informative blog on the subject, but she covers only the IR Lagoon: Jacqui Thurlow-Lippisch | Indian River Lagoon
There is a strong movement on the east coast
of FL to undo all of the Army Corps of Engineers' disastrous work to drain the Everglades with these man-made canals/Caloosahatchee/St. Lucie outlets to the sea, and Send The Water South to be naturally cleaned by the Everglades, but I think that with the political climate we have now this will never be accomplished. The Gulf and Atlantic will absorb it all in about a hundred years anyway, when all of South FL is submerged.