Right. You might have better luck making it shallower OR deeper. Let me explain...
1. Shallow sand beds / bare bottom tanks are nice because they do not trap detritus.
2. Deep sand beds (like 6 inches and deeper) are nice because they generate anaerobic zones where bacterial species flourish that, in the abscence of oxygen, can remove nitrates from your system.
If your sandbed is in between, it can (in theory) trap detritus without any denitrification benefit. You have three options:
1. You might carefully vacuum your bed your bed / do water changes to get the detritus / nitrates out and see what happens. Go slow, sometimes when people really stir up a previously undisturbed sandbed, they have problems. I know plenty of people with "in between" sandbeds that do fine with a little maintenance.
2. Remove sand to 1 inch depth or bare bottom and groom it frequently to keep it detritus free. Lots of circulation will help.
3. Add sand to make it six inches or deeper.