Ammonia (very toxic), Nitrites (less toxic), and Nitrates (not toxic unless concentration is high, keep below 25 PPM) are read in Parts Per Million. What kind of test are you using? If paper strips they just serve as warning and are inaccurate. Presence of Nitrites (and possibly Ammonia) indicate either no filter or an uncycled one.

If no filter, suggest 25% water change daily and do not overfeed. If you have a cycled filter; 25% a week should work. Beneficial bacteria will also live on substrate; but if you cleaned that in tap water, they all died. Gravel is an impaction risk if ingested. Suggest either bare bottom or very fine sugar sized sand.

If you have a filter, the media should be cleaned during weekly water change with tank water you are removing. When replacing media some of old one must be left in filter (i.e. don't replace filter pad/foam at same time as other bio-media in filter). Good luck !