My first question would be is there any external indication of them such as air holes or anything else that you can assess from the surface? I would think that if there is, you could use transects and a quadrat. If you need to dive for them you can obviously make a weighted quadrat by filling pvc pipe with sand and gluing it together. Then take an area and lay out transects and and randomly choose different lengths along each transect to put the quadrat down and that will give you an estimate of density. If you actually need to extract them from the mud, I imagine that varies by species and you could make due with a grab sampler of the right size, something on the small end I would imagine. That way you aren't dredging up tons and tons of mud to sort through. If they are even rarer than I imagine, you could just lay out transects and swim them until you see something and do away with the quadrat. Hope this helps.
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