Subsurface zones of groundwater and surface water mixing (hyporheic zones) are regions of enhanced rates of biogeochemical cycling, but ecological processes influencing hyporheic microbiomes through space and time remain unknown. We sampled attached and planktonic microbiomes in the Columbia River hyporheic zone across seasonal hydrologic change within three hydrologically-connected, yet physicochemically-distinct geographic zones (inland, nearshore, river). Although microbiomes remained dissimilar through time across all zones and habitat types (attached vs. planktonic), consistent presence of certain heterotrophic taxa suggested dispersal and/or common selective pressures among all zones. We used statistical null models and co-occurrence network analysis, respectively, to demonstrate a pronounced impact of deterministic assembly on microbiomes in all data subsets and to elucidate taxa most affected by these processes. The composition of one network cluster of nearshore organisms exhibited a seasonal shift from heterotrophic to autotrophic microorganisms, and the abundance of taxa within this cluster also correlated positively with active microbial biomass and metabolism, possibly indicating that these taxa have strong influences over biogeochemical reactions within the hyporheic zone. Taken together, our research demonstrates a predominant role for deterministic assembly across highly-connected environments and provides insight into niche dynamics associated with seasonal changes in hyporheic microbiome composition and metabolism.