If I understand your question correctly, a simple way is to measure the community respiration (i.e. O2 consumption as a proxy for energy consumption) in the water column vs. the sediment. This can be done as simple respiration chamber incubations.

You might find this useful:

https://www.researchgate.net/publication/257350828_Surviving_in_a_Marine_Desert_The_Sponge_Loop_Retains_Resources_Within_Coral_Reefs

Article Surviving in a Marine Desert: The Sponge Loop Retains Resour...

Colleagues, thank you very much for your help!