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Inorganic nitrogen (N) transformations and removal in aquatic sediments are microbially mediated, and rates influence N-transport. In this study we related physicochemical properties of a large Great Lakes embayment, the St. Louis River Estuary (SLRE) of western Lake Superior, to sediment N-transformation rates. We tested for associations among rates and N-inputs, vegetation biomass, and temperature. We measured rates of nitrification (NIT), unamended base denitrification (DeNIT), and potential denitrification [denitrifying enzyme activity (DEA)] in 2011 and 2012 across spatial and depth zones. In vegetated habitats, NIT and DeNIT rates were highest in deep (ca. 2 m) water (249 and 2111 mg N m(-2) d(-1), respectively) and in the upper and lower reaches of the SLRE (>126 and 274 mg N m(-2) d(-1), respectively). Rates of DEA were similar among zones. In 2012, NIT, DeNIT, and DEA rates were highest in July, May, and June, respectively. System-wide, we observed highest NIT (223 and 287 mg Nm(-2) d(-1)) and DeNIT (77 and 64 mg N m(-2) d(-1)) rates in the harbor and from deep water, respectively. Amendment with NO3- enhanced DeNIT rates more than carbon amendment; however, DeNIT and NIT rates were inversely related, suggesting the two processes are decoupled in sediments. Average proportion of N2O released during DEA (23-54%) was greater than from DeNIT (0-41%). Nitrogen cycling rates were spatially and temporally variable, but we modeled how alterations to water depth and N-inputs may impact DeNIT rates. A large flood occurred in 2012 which temporarily altered water chemistry and sediment nitrogen cycling. Published by Elsevier BM, on behalf of International Association for Great Lakes Research.