Sorry to hear about the loss.

That rain event is most likely the cause of the die off, but lets see what others have to say. I have heard, and experienced, that the bigger fish tend to expire first when a bad water event happens like lack of dissolved oxygen, so maybe you didn't have a total die-off.

Excerpt from Robert Crais' "The Monkey's Raincoat:"
"She took another microscopic bite of her sandwich, then pushed it away. Maybe she absorbed nutrients from her surroundings."