Application of a hydrogeologic computer model underscored the importance of geomorphic controls on groundwater and surface-water flow dynamics in the Nyack Floodplain, a montane alluvial floodplain in Montana, USA. The model represented the floodplain as a hierarchy of geomorphic patches, which facilitated analysis of model results using independent (predictor) variables at multiple scales. The analyses revealed that geomorphic structures at various spatial scales interact with the flow regime to influence the direction, magnitude, and stability of hyporheic flow within individual floodplain patches. Specifically: 1) the hydrologic flow network within the hyporheic zone is more responsive to seasonal changes in river discharge if floodplain topography is complex and aquifer properties are heterogeneous, 2) simplification of internal patch structure across the floodplain eliminates the influence of fine-scale geomorphic structures on the stability of groundwater flow paths, although the influence of patch context remains, and 3) incremental changes in river discharge can abruptly and substantially restructure the relationship between river discharge and groundwater flow patterns when events such as inundation of previously dry flood channels occur on the floodplain. We believe that ecological theories of biodiversity can be used to understand interactions among geomorphic variation, hydrologic dynamics, and the maintenance of biodiversity in the hyporheic zone if abrupt reorganization and other variations in groundwater flow paths act as disturbances to hyporheic communities. From this perspective, we used model results to develop 4 hypotheses describing the potential for causal linkages among floodplain geomorphology, hyporheic flow-path variation, hyporheic habitat diversity/stability, and hyporheic community diversity.