clean it in a bucket of aquarium water.
Hi,get an aquarium gravel vacuum, be careful not to stir up the gravel too much, or hold the pipe you are siphoning from just high enough to suck up the mulm but not low enough to suck up the gravel.
specifically because you have large gravel, and large poop factories for fish,Mind you I only have river-rock as a bed in my aquarium and do not have layers of different sub-straight. I also have Goldfish in my tank.