Interesting observation. I hope it's not chemical runoff or pH. I don't know the area, but a few notions cross my mind FWIW.

I'd echo previous questions about invertibrates -- insects, snails, water bugs of any kind. These, and algae/water plants, are the foundation of the food chain.

Sometimes, very deep lakes fed by very cold streams will have very short "growing" seasons, during which the food chain will bloom and disappear in a few warm weeks in later summer.

Development and excessive traffic can sometimes isolate lakes from ungulate/predator corridors.

Last, did you see evidence of rodents at all? Sometimes the land-based food chain depends on these little critters. I've often suspected that a dozen mouse traps and a jar of peanut butter would net more calories per day, consistently, than a firearm.