Sounds like a new tank....is it even cycled yet? The gravel is probably an important part of your Bio filter....I would remove the fish with water skimmed off top into bucket and then vacuum the gravel down to half tank or less.....remove gravel....RINSE SAND until it drains clean!!!! Then scape and return and fill er up.....Do lots of testing in the days after and dose with Prime when changing water or if ammonia or nitrite spike. Good luck!! Everyone should be fine!!
I switched gravel and was worried about losing the bacteria in the old gravel. So I rinsed it in old tank water, tied it up in a nylon stocking, and left it in the corner of the tank for a couple of weeks after changing the substrate. By then I figured the bacteria must have sufficiently grown in the new gravel and took the old stuff out.
I'm not sure if I was worrying too much, but it set my mind at rest, and no fish were lost in the substrate change.