AbstractEfforts to reduce riverine phosphorus (P) loads have not been as fruitful as expected or hoped. One reason for the failure of these efforts appears to be that models used for watershed P management have understated and misrepresented the role of in‐stream processes in shaping watershed P export. Here, we update the latest release of the Soil and Water Assessment Tool (SWAT+), a widely used watershed management model, to better represent in‐stream P retention and remobilization (SWAT+P.R&R). We add new streambed pools where P is stored and tracked, and we incorporate three new processes driving in‐stream P dynamics: (a) deposition and resuspension of sediment‐associated P, (b) diffusion of dissolved P between the water column and streambed, and (c) adsorption and desorption of mineral P. The objective of this modeling work is to provide a diagnostic tool that enables researchers to challenge existing assumptions regarding how watersheds store, transform, and transport P. Here, in a first diagnostic analysis, SWAT+P.R&R helps reconcile in‐stream P retention theory (that P is retained at low flows and remobilized at high flows) and a discordant data set in our validation watershed. SWAT+P.R&R results (a) clarify that the theorized relationship between P retention and flow is only valid (for this point‐source affected testbed, at least) at the temporal scale of a single rising‐or‐falling hydrograph limb and (b) illustrate that hysteresis obscures the relationship at longer temporal scales. Future work using SWAT+P.R&R could further challenge assumptions regarding timescales of in‐stream P legacies and sources of P load variability.