Increasing levels of nitrogen (N) in freshwaters can threaten water quality. The removal of N by wetlands and streams is of particular interest in agricultural landscapes because N export has been implicated in creating low-oxygen zones and harmful algal blooms in coastal waters. Studies indicate that most of the anthropogenic N added to watersheds (e.g., as fertilizer) is lost in transit through the ground and surface waters of the hydrologic system before reaching the oceans. Nitrate is the most important N form moving through hydrologic systems. To date, the majority of nitrate removal has been attributed to a bacterial process called respiratory denitrification, and much of this removal is suspected to occur in small streams and wetlands. However, recent research has highlighted other bacterial processes that may be important in removing nitrate from freshwater systems, including dissimilatory nitrate reduction to ammonium (DNRA), sulfide oxidation coupled to denitrification, and abiotic conversion to DON via iron. The goal of this research is to assess the prevalence and importance of these alternative pathways of nitrate removal in freshwater ecosystems. The most general hypothesis is that various freshwater systems will differ in the relative importance of alternative processes, and that these differences will arise primarily from the system's biogeochemical and hydrological setting. The removal pathways will be quantified using landscape survey and stable isotope techniques in a variety of freshwater ecosystems. The results will have implications for the management of ecosystems to promote nitrate removal.