Mesh refinement near river corridors is commonly deployed to resolve topographic details important for accurately representing riverine flow dynamics in watershed-scale spatially distributed integrated hydrology models. However, this increased accuracy comes with higher computational costs due to larger mesh and smaller time steps resulting from small mesh cells. We present a novel stream-aligned mixed-polygonal meshing approach that resolves river-corridor topography efficiently by placing long quadrilateral cells along the mapped center lines of the rivers and standard Triangulated Irregular Network (TIN) mesh in the rest of the domain. Our integrated hydrology simulations using mixed-polyhedral mesh generated from the mixed-polygonal approach closely match those using a highly refined extruded-TIN mesh but with a 96.43% reduction in the number of mesh cells and a 99.75% reduction in CPU hours. Conversely, coarser extruded-TIN meshes, due to poor water conveyance relative to the refined mesh simulations, yielded lower peak flows, longer recession curves, and higher inundation fractions.The creation of this mixed-polyhedral mesh is implemented within the Watershed Workflow tool, a Python-based workflow library for watershed simulation. We also implemented a layered process of hydrologic conditioning specific to the cells in the river corridor, which are explicitly meshed within the mixed-polyhedral mesh. The hydrologic conditioning enforces monotonic topographic gradients, removes spurious obstructions, and allows for burning-in depths of the river cells based on ancillary information. This approach paves the way for efficiently modeling narrow engineered channels and specifying river-specific hydrodynamic details and biogeochemical processes.