Uh...there were massive algal blooms ...red tides... When the Spanish arrived, long before there were settlers, leaky septic tanks, and power boats. Either the local Indians (who ate manatees, by the way) were huge polluters or else red tide is a natural and not infrequent occurrence most likely due to temperature (this year was very hot and much wetter than usual) and current speeds and direction.
Fertilizer runoff from sugar cane field is a large factor in red tide algae blooms. Nutrient rich water coming down the caloosahatchee river is essentially the problem.