Hydrologic and water quality models are often used to understand and simulate non-point source nutrient inputs to receiving waterbodies afflicted by eutrophication. The most widely used hydrologic-water quality model for estimating non-point source nutrient loads from agricultural uplands is the Soil and Water Assessment Tool (SWAT). SWAT uses the QUAL-2E 1-dimensional steady-state model to simulate in-stream processes that govern the transport of nutrients through channels and rivers. However, the instream-solute transport routine within SWAT is limited in predicting phosphorus cycling and algal dynamics. In this study, we improve the in-stream module of SWAT+, a restructured version of SWAT. We apply the modified SWAT+ to the Western Lake Erie Basin to examine how improved representation of the in-stream module influences nutrient dynamics from the edge-of-field through streams and to the watershed outlet. Our source code modifications focus on improving the representation of phosphorus exchange between the stream bed and the water column. This phosphorus exchange is governed by the equilibrium phosphorus concentration (EPC), which determines whether the stream bed is a phosphorus source or sink, and a phosphorus transformation coefficient which determines the rate of P exchange. These improvements to the in-stream routine within SWAT+ will aid decision-makers in understanding the time lags and management levers needed to achieve water quality targets for large basins.