As a long time scuba
diver and former resident of Melbourne, Fl, I can tell you that this phenomenon is not new and occurred regularly during the 1960s. This was a time when we had no cruise
ships at Port Canaveral and only a few in south Florida
. The speculation about upwelling is well founded. When diving
off shore from the Melbourne area south to Ft Pierce, it was common in the summer to hit a thermocline near the bottom with a lot of suspended particulates (filamentous algae). On occasion a sustained offshore wind
would push out the warm surface waters and bring this layer to the surface near the beach. There has recently been a lot of beach renourishment projects going on in the area. I don't know if any are active at the moment but they introduce a tremendous amount of particulates into the water. This could be another source. All the speculation about sewage and runoff can be pretty much discounted. All of the storm sewers and treatment plants in that area empty into the indian river and flow out of sebastian inlet. If you've ever seen the inlet from the air you would note that the outflowing tide tends to turn south. This is probably due in part to the Coriolis effect and the generally southward flowing current
close to shore sout of Cape Canaveral to about Ft. Pierce. Outflow here would have little effect on water quality on the ocean side in Melbourne.