Recently that bay was in the news because of some type of invasive organism in the water, most likely due to untreated sewage.
Although when I was there I hardly got any poop in my mouth at all.
Yikes! We never swam in PR. The water looked dirty everywhere. Then we took a puddle jumper to St. Croix where my cousin was living. He set us up with a day trip on a catamaran to Buck island for a day of snorkeling. Wow that was amazing.