Biogeochemical cycling within river ecosystems is strongly influenced by geomorphic and hydrologic dynamics. To scale point observations of temperature and dissolved oxygen (DO) to a hydrologically complex and dynamic three-dimensional river-floodplain-aquifer system, we integrated empirical models of temperature and biotic oxygen utilization with a recently published hydrogeomorphic model. The hydrogeomorphic model simulates channel flow, floodplain inundation, and surface-subsurface water exchange on the 16 km2 Nyack Floodplain, Middle Fork Flathead River, Montana, USA. Model results were compared to observed data sets of DO to test the hypothesis that complexity in spatiotemporal patterns of biogeochemistry emerges from a comparatively simple representation of biogeochemical processes operating within a multidimensional hydrologic system. The model explained 58% of the variance in 820 DO measurements that spanned the study site longitudinally, laterally, vertically, and across river discharge conditions and seasons. We also used model results to illustrate spatial and temporal trends of temperature and DO dynamics within the shallow alluvial aquifer, which is an extensive hyporheic zone because subsurface alluvial flow paths are recharged primarily by channel water. Our results underscore the importance of geomorphic, hydrologic, and temperature dynamics in driving river ecosystem processes, and they demonstrate how a realistic representation of a river's physical template, combined with simple biogeochemical models, can explain complex patterns of solute availability.