Macroinvertebrate samples were collected from streams tributary to Honnedaga Lake and from the Middle Branch of the Black River during 2012-2016 and analyzed for methylmercury concentrations and for stable isotope ratios of nitrogen and carbon. Macroinvertebrates were identified in the field, and the level of taxonomic resolution varied from order to species; most taxa were identified to the family level. Specimens were field-processed into composite samples, field-frozen, and submitted to the mercury laboratory for freeze-drying and analysis. Subsamples were then submitted to the stable isotope laboratory for analysis of nitrogen and carbon isotope ratios. This database contains the resulting data and associated information for these composite samples of whole macroinvertebrates.