Legacy nutrient accumulation from excess anthropogenic inputs has become a serious environmental issue in many watersheds worldwide. In this review, we provide a systematic overview of sources, legacy nutrient pools, watershed-scale water quality models, and agronomic and environmental implications of legacy nitrogen and phosphorus pools. Hydrological, biogeochemical, and anthropogenic factors exert interacting controls on legacy nutrient dynamics in soils, sediments, and vadose zone/groundwater. Most current watershed models do not effectively incorporate legacy nutrient dynamics, while models that consider legacy effect often have high uncertainty in their treatment of legacy nutrient dynamics. In many intensively managed watersheds, legacy nutrients are a dominant and long-term (> 10 years) source of nutrients to receiving waters, as well as a potentially important nutrient source for crop production. Many existing beneficial management measures have limitations for reducing legacy nutrient losses to surface waters due to appreciable differences in legacy nutrient forms, watershed storage locations, and temporal dynamics compared to those of contemporary nutrient inputs. Recognizing the importance of legacy nutrients is necessary for developing sustainable watershed nutrient management plans for future food, bioenergy, and water security. These plans require strategies to maximize use of legacy nutrient resources to minimize their loss to the atmosphere (e.g., N2O emissions) and surface waters. Finally, this synthesis identified future research needs for improving the understanding, utilization, and mitigation of watershed legacy nutrient pools.