Human activities have increased the availability of reactive nitrogen in many ecosystems, leading to negative impacts on human health, biodiversity, and water quality. Freshwater ecosystems, including lakes, streams, and wetlands, are a large global sink for reactive nitrogen, but factors that determine the efficacy of freshwater nitrogen removal rates are poorly known. Using a global lake data set, we show that the availability of phosphorus, a limiting nutrient, affects both annual nitrogen removal rate and efficiency. This result indicates that increased phosphorus inputs from human activities have stimulated nitrogen removal processes in many lakes. Recent management-driven reductions in phosphorus availability promote water column accumulation and export of nitrogen from large lakes, an unintended consequence of single-element management that argues for greater control of nitrogen as well as phosphorus sources.