I have been dealing with the same problem, and since we have pine tress around the pool, I thought it could be dust or dirt coming from them. However, I just spoke to someone at my local pool store and they told me most likely it is guano, that there are bats in those tress, but to me it still looks more like dust or sand. I had the sand replaced, vacuum every day, and after a two or three hours the brown spots are back! I have to say though, after changing the sand in the filter and treating the water properly, it looks much better, but still dealing with brown spots. Had any of you heard about guano in the pool?