While there is great interest in managing agricultural landscapes with riparian zones, wetlands and other practices to improve water quality, there is great uncertainty about the effects of these processes on greenhouse gas emissions.  There is particular concern about the creation of anaerobic areas to foster denitrification, the microbial conversion of nitrate (the most common form of pollutant nitrogen) into nitrogen gases.  These areas can also be important sources of nitrous oxide (one of the nitrogen gases produced by denitrification) and methane (a common product of anaerobic environments).  Determining the net greenhouse gas impacts of landscape conservation practices requires quantification of several spatially and temporally variable phenomena including, 1) comparison of the greenhouse gas emissions of the original, current and potential future states of the ecosystems being managed for water quality, 2) determination of if hydrologic flowpaths carrying water pollutants from uplands interact with specific landscape areas to create hotspots and/or hot moments of pollutant removal and/or greenhouse gas production, 3) comparison of the greenhouse gas emissions of managed landscape areas with emissions that would occur if pollutants are allowed to flow farther downstream, and 4) quantification of the full net greenhouse forcing associated with carbon sequestration in soils and vegetation and any increases or decreases in carbon dioxide, nitrous oxide and methane fluxes.  Comprehensive evaluations are necessary to minimize tradeoffs between water quality and greenhouse forcing objectives in agricultural landscapes.