Nearly all freshwaters and coastal zones of the US are degraded from inputs of excess reactive nitrogen (Nr), sources of which are runoff, atmospheric N deposition, and imported food and feed. Some major adverse effects include harmful algal blooms, hypoxia of fresh and coastal waters, ocean acidification, long-term harm to human health, and increased emissions of greenhouse gases. Nitrogen fluxes to coastal areas and emissions of nitrous oxide from waters have increased in response to N inputs. Denitrification and sedimentation of organic N to sediments are important processes that divert N from downstream transport. Aquatic ecosystems are particularly important denitrification hotspots. Carbon storage in sediments is enhanced by Nr, but whether carbon is permanently buried is unknown. The effect of climate change on N transport and processing in fresh and coastal waters will be felt most strongly through changes to the hydrologic cycle, whereas N loading is mostly climate-independent. Alterations in precipitation amount and dynamics will alter runoff, thereby influencing both rates of Nr inputs to aquatic ecosystems and groundwater and the water residence times that affect Nr removal within aquatic systems. Both infrastructure and climate change alter the landscape connectivity and hydrologic residence time that are essential to denitrification. While Nr inputs to and removal rates from aquatic systems are influenced by climate and management, reduction of N inputs from their source will be the most effective means to prevent or to minimize environmental and economic impacts of excess Nr to the nation’s water resources.