When a substrate is too thick, water (and thus oxygen) can't reach the deepest parts, allowing anaerobic bacteria (bacteria that can't live in the presence of oxygen) to colonize there. Some anaerobic bacteria are good and will lower your nitrate levels, but others will produce sulfuric gas that can (theoretically) hurt your fish if the substrate is disturbed. I'm not sure, but I think it can also damage plant roots.
There's a little bit of debate on whether or not anaerobic spots are actually harmful and what is the best way to prevent them. You can stir the substrate weekly, get trumpet snails to burrow in it (however, these can become a nuisance), or plant thickly and let the plant roots oxygenate it.
My fish change their own water... from clean to dirty.