I find that lawyers are the easiest members of the benthic community to study.  You might try putting out big plates of free bacon at a legal function and see how much they eat before they turn blue.  You could then roughly calculate the effect levels and reduce those an order of magnitude to ensure the safety of the more desirable benthics.  

But, of course, you question also related to "problem" levels of nitrites.  I'm not sure that making lawyers turn blue and keel over would meet the definition of a "problem."  

You can probably do some ecotoxicological experiments with benthic invertebrates, such as Ostracoda (there are some commercial kits with eggs you can hatch), and compare the hatching rate and survival rate when cultured in containers with your sediment or with other (same type of ) sediment with less N load. But still, there might probably be other chemical or biological components that could be affecting the differential survival.

I wondered if Arango et al (Freshwater Biol) might help get a sense of how much may be leaching without having to do any additional measurements (attached).  Especially if the DOC etc of the water is known.  If there is any potential for additional testing I would be tempted to do in-situ bioassays (e.g., Phil Williams' work on in-situ bioassays with Lumbriculus).      

You can test bulk sediment samples using Hyalella and Chironomids using EPA "Methods for assessing the toxicity and bioaccumulation of contaminants in sediments."