The increasing trend in riverine phosphorus (P) loads resulting from anthropogenic inputs has gained wide attention because of the well-known role of P in eutrophication. So far, however, there is still limited scientific understanding of anthropogenic P inputs and their impacts on riverine flux in river reaches along the upstream-to-downstream continuum. Here we investigated P budgets in a series of nested watersheds draining into Hongze Lake of China and developed an empirical function to describe the relationship between anthropogenic inputs and riverine P fluxes. Our results indicated that there are obvious gradients regarding P budgets in response to changes in human activities. Fertilizer application and food and feed P import was always the dominant source of P inputs in all sections, followed by nonfood P. Further interpretation using the model revealed the processes of P loading to the lake. About 2%–9% of anthropogenic P inputs are transported from the various sections into the corresponding tributaries of the river systems, depending upon local precipitation rates. Of this amount, around 41%–95% is delivered to the main stem of the Huai River after in-stream attenuation in its tributaries. Ultimately, 55%–86% of the P loads delivered to different locations of the main stem are transported into the receiving lake of the downstream, due to additional losses in the main stem. An integrated P management strategy that considers the gradients of P loss along the upstream-to-downstream continuum is required to assess and optimize P management to protect the region's freshwater resource.