The first time I did it was when I had to move my tank. And I figured while I have the thing torn apart, might as well give it a good cleaning... And you are absolutely right, it was scary. I could barely see any glass on the bottom because it was covered with @#$%. I mean it was BAD. That's why I thought that might be your source. If you mean by bad for the fish, you mean with hurting the cycle, all you have to do is when you are emptying the tank, keep anywhere from 25-50% of the old aquarium water and put the gravel in that water, don't wash it. then you can clean your tank, and put the wet, uncleaned rocks back in, add the old aquarium water, then add new water. Any spikes should be minimal, in essence, because the gravel remains in the actual aquarium water, it is like doing a 50% water change. If you want to minimize spikes even more, keep more of the old water. It's a lot of work, but it might be worth a try. But mine was only a 10 gal so it made it a lot easier....