Do you have plants rooted in your substrate, and how deep and what size grains does your substrate have?
If you have a couple of inces of very fine sand then you cold get anaerobic decomposition in it a have bubbles of hydrogen sulphide building up. If you have a grain size that lets water circulate through then this won't happen.
If you have larger grains then fish poo and decaying plant matter can get through the gaps and decompose to form nitrates.
If you have plants rooted in the gravel then the roots will feed off the mulm building up and use the nitrates as fertiliser.
If you have gravel and plants you won't want to disturb the roots.... let them do their thing.
One school of thought is that Malaysian Trumpet Snails (MTS) will dig through the gravel, cleaning and aerating it as they rootle, but won't disturb the roots of plants.
I have gravel and plants and haven't hoovered anything more than the gravel surface for at least a year and everything seems to be fine. I added some MTS about 3 weeks ago - the results are not yet in, but I will post my thoughts as soon as I have any. (Results, that is. Not thoughts. I don't have those
)
So - very fine grains need disturbing and cleaning to avoid toxicity.
'Normal' grain sizes without plants need gravel cleaning every now and then.
'Normal' grain sizes with plants can be left alone, just clean the surface. As for MTS..... watch this space!
If you have an under-layer of compost with gravel on top, then the mulm should sink through the gravel layer to keep the under-layer refreshed with nutrients.