Biocomplexity is an emergent property of ecosystems that captures the interplay of structures and processes at multiple scales. These interactions can establish a dynamic habitat template that serves as a filter to define ecological organization across landscapes. Studies of biocomplexity in floodplain rivers typically focus on hydrological variability or geomorphic heterogeneity separately, with their interactions being an output rather than the direct focus of investigations. This study examines the interaction of hydrological variability and geomorphic heterogeneity across 25 off‐channel habitats (OCHs) of the Upper Mississippi River, USA. Questions posed were as follows: What are the interactive effects of hydrological variability and geomorphic heterogeneity shaping the physical habitat template of OCHs? and How does the organization of the physical habitat template influence fish community composition within OCHs? Three distinct OCH groups emerged from this study: where hydrological variability defined Group 1 (Lake group); Group 2 was organized via geomorphic heterogeneity (Backwater group); and a combination of hydrological and geomorphological variables defined Group 3 (Slackwater group). Thus, the differential interaction of hydrology and geomorphology defined the dynamic physical habitat template of OCHs in this riverine landscape. No significant difference between the association matrices of the hydrogeomorphic template and fish community composition for the 25 OCH sites was recorded. A priori grouping of fish into the three OCH groups revealed marked differences in fish community composition. A subset of hydrogeomorphic variables that defined the physical character of the OCHs acted as an environmental filter for the fish community composition of the three OCH groups. A conceptual model explaining hydrogeomorphic–ecological interactions across the OCHs of this floodplain river system is provided.