Extended end-member mixing analysis (E-EMMA) is presented as a novel empirical method for exploring phosphorus (P) retention and release in rivers and watersheds, as an aid to water-quality management. E-EMMA offers a simple and versatile tool that relies solely on routinely measured P concentration and flow data. E-EMMA was applied to two river systems: the Thames (U.K.) and Sandusky River (U.S.), which drain similar watershed areas but have contrasting dominant P sources and hydrology. For both the Thames and Sandusky, P fluxes at the watershed outlets were strongly influenced by processes that retain and cycle P. However, patterns of P retention were markedly different for the two rivers, linked to differences in P sources and speciation, hydrology and land use. On an annual timescale, up to 48% of the P flux was retained for the Sandusky and up to 14% for the Thames. Under ecologically critical low-flow periods, up to 93% of the P flux was retained for the Sandusky and up to 42% for the Thames. In the main River Thames and the Sandusky River, in-stream processes under low flows were capable of regulating the delivery of P and modifying the timing of delivery in a way that may help to reduce ecological impacts to downstream river reaches, by reducing ambient P concentrations at times of greatest river eutrophication risk. The results also suggest that by moving toward cleaner rivers and improved ecosystem health, the efficiency of P retention may actually increase.