His research focuses on terrestrial biogeochemistry with a focus on nitrogen dynamics, especially gases. Projects have ranged across multiple scales from microbial/molecular scale analyses to field/ecosystem scale measurement of fluxes using geochemical and isotope approaches, to landscape and regional scale work using remote sensing, geographic information systems and simulation models. Much of his research is focused at two National Science Foundation funded Long Term Ecological Research (LTER) sites; Hubbard Brook, New Hampshire and Baltimore, MD.
He has authored over 300 publications, with more than 85 as primary author. Groffman was a Convening Lead Author for the 2013 U.S. National Climate Assessment Chapter on Ecosystems, Biodiversity and Ecosystem Services and a lead author for the Second (Wetlands) and Third (North America) Assessment Reports of the Intergovernmental Program on Climate Change (IPCC).