Depends on what substrate... If it's gravel, before you do a water change, take out like 25%-50% of the gravel and replace it with the new gravel, then do a water change. Do another water change in a week and replace the rest of the gravel.
If it's sand, that's trickier... I would put some gravel in a pantyhose stocking and then take out all the gravel and put in the sand. I would recommend putting the fish in a butcket during this time. Do your water change, then after your done and the sand has settled, place the fish back with the stocking of gravel. Wait several days and take out the stocking.