I would not worry about cedar any more than I would about pine, oak, or others. The concentration of vapors seem to be the problem with cedar. As long as you have good ventilation that should not be a problem.
I admit I'm a little warped. I grew up on a farm where the chickens, dogs, horses, cats, and cattle drank from a farm pond. Wild birds and other wild animals drank from it. Fish, turtles, frogs, and various bugs lived in it. I imagine it would gross out many people on this forum as it was far from pristine. It did not seem to bother the animals. But I believe we should try to keep our animals' water "clean". Bad things that have a life cycle of a few days can multiply in "dirty" water so I dump mine a minimum of every two days. Usually every day. It's easy insurance.
I do not see any benefit in having anything in the water: plant debris, dirt, poop, anything. So I try to keep the water clean. I don't know how the debris is getting in your water. If it is falling in you may need to move it or put up some kind of shield. If they are scratching it in (my main problem) it may help to raise it.
I do not see this as a life or death issue but I would try to remedy it. Good luck!