Floodplains are essential ecosystems that provide a variety of economic, hydrologic, and ecologic services. Within floodplains, surface water‐groundwater exchange plays an important role in facilitating biogeochemical processes and can have a strong influence on stream hydrology through infiltration or discharge of water. These functions can be difficult to assess due to the heterogeneity of floodplains and monitoring constraints, so numerical models are useful tools to estimate fluxes, especially at large spatial extents. In this study, we use the SWAT+ (Soil and Water Assessment Tool) ecohydrological model to quantify magnitudes and spatiotemporal patterns of floodplain surface water‐groundwater exchange in a mountainous watershed using an updated version of the gwflow module that directly calculates floodplain‐aquifer exchange rates during periods of floodplain inundation. The gwflow module is a spatially distributed groundwater modelling subroutine within the SWAT+ code that uses a gridded network and physically based equations to predict groundwater storage, groundwater head, and groundwater fluxes. We used SWAT+ to model the 7516 km2 Colorado River headwaters watershed and streamflow data from USGS gages for calibration and testing. Models that included floodplain‐groundwater interactions outperformed those without such interactions and provided valuable information about floodplain exchange rates and volumes. Our analyses on the location of floodplain fluxes in the watershed also show that wider areas of floodplains, “beads” (e.g., like beads on a necklace), exchanged a higher net and per area volume of water, as well as higher rates of exchange, compared to narrower areas, “strings.” Study results show that floodplain channel‐groundwater exchange is a valuable process to include in hydrologic models, and model outputs could inform land conservation practises by indicating priority locations, such as beads, where substantial hydrologic exchange occurs.