This study explores microbial community structure in managed aquifer recharge (MAR) systems across both laboratory and field scales. Two field sites, the Taif River (Taif, Saudi Arabia) and South Platte River (Colorado), were selected as geographically distinct MAR systems. Samples derived from unsaturated riverbed, saturated-shallow-infiltration (depth, 1 to 2 cm), and intermediate-infiltration (depth, 10 to 50 cm) zones were collected. Complementary laboratory-scale sediment columns representing low (0.6 mg/liter) and moderate (5 mg/liter) dissolved organic carbon (DOC) concentrations were used to further query the influence of DOC and depth on microbial assemblages. Microbial density was positively correlated with the DOC concentration, while diversity was negatively correlated at both the laboratory and field scales. Microbial communities derived from analogous sampling zones in each river were not phylogenetically significantly different on phylum, class, genus, and species levels, as determined by 16S rRNA gene pyrosequencing, suggesting that geography and season exerted less sway than aqueous geochemical properties. When field-scale communities derived from the Taif and South Platte River sediments were grouped together, principal coordinate analysis revealed distinct clusters with regard to the three sample zones (unsaturated, shallow, and intermediate saturated) and, further, with respect to DOC concentration. An analogous trend as a function of depth and corresponding DOC loss was observed in column studies. Canonical correspondence analysis suggests that microbial classes Betaproteobacteria and Gammaproteobacteria are positively correlated with DOC concentration. Our combined analyses at both the laboratory and field scales suggest that DOC may exert a strong influence on microbial community composition and diversity in MAR saturated zones.