MIAMI — Thousands of fish, eels and turtles are dying, sometimes as far as the eye can see, in parts of southwest Florida. Just this week, one of several lifeless manatees was pulled from the water.

A toxic algae called “Heterosigma akashiwo” is blooming in San Francisco Bay, causing the water to look murky and brown and posing a danger to local marine life. The ongoing bloom could kill fish and ...