Quote Originally Posted by Rangeball
It sure sounds like yellow algae.
Ahhh, ignorance was bliss... It appears we have a similar thing happening in our pool as well this year. It's the first time I've noticed the brownish "mud" on the pool floor and it matches the descriptions here.
I've also noticed that the shade-side wall of our pool (fiberglass) is slightly more yellow than the sun side in an area that was bypassed by the return flow.
Lessons learned: I'll be adopting Matt's 3rd year approach to killing off whatever this stuff is, and hope the shock will also clear out what may be "yellow algae sheets" (ewww!) on the shade wall. I'll also be adding a return eyeball to direct flow (and chlorine or other treatments) towards that wall.

Thanks for a helpful thread & I hope the heavy shock/brush routine works out!