Benthic flux procedures may be useful for the study to understand the toxicity of the sediments. Magnetic properties will also be a good proxy to understand the contamination.
"What to do with them", does that mean how to treat them, disgard them, or study them?
In general, high OM in polluted sediments means low availability. But you will need quite some more information that just the OM content.
You could have a look at the Dutch guidelines for treatment of sediments. There, the treatment really depends wether you 'Touch" them, or leave them where they are. The first assessment would be to get some total content measurements of the expected pollutants.
The processes of eutrophic-dystrophy in inland waters are related to the amount of oxygen available for the oxidation of nutrients. In Italy we applied this simple concept for rehabilitation of the lakes Flegrei, on the Campanian coast. A mathematical model is made specifically explained to us that it was possible the restoration of natural areas, only reopening the mouths of emissaries of the lakes to facilitate the flow of oxygenated sea water, whose oxygen content was enough to encourage the process of oxidation. It 'clear that a coastal lagoon is not a river, where the release of oxygen is difficult and purification processes, through purifiers, are extremely expensive
I think it would be helpful to have some additional information from Martha. A bit of background and a more specific question would lead to more focused helpful answers.
e.g. what kind of contamination are you dealing with? Is the OM naturally occurring or a consequence of the contamination? Are you attempting to study them or remediate them? What sort of guidelines are you looking for? etc.
I hope that helps you get the answers that you're looking for.