Hydraulic connection between channels and floodplains (“connectivity”) is a fundamental determinant of ecosystem function in large floodplain rivers. Factors controlling material processing in these rivers depend not only on the degree of connectivity but also on the sediment conditions, nutrient loads, and source. Nutrient cycling in the nutrient‐rich upper Mississippi River (MISS) is relatively well studied, whereas that of less eutrophic tributaries is not (e.g., St Croix River; SACN). We examined components of nitrogen cycling in 2 floodplain rivers of contrasting nutrient enrichment and catchment land use to test the hypothesis that N‐cycling rates will be greater in the MISS with elevated nutrient loads and productivity in contrast to the relatively nutrient‐poor SACN. Nitrate (NO₃⁻‐N) concentrations were greatest in flowing habitats in the MISS and often undetectable in isolated backwaters except where groundwater inputs occurred. In the SACN, NO₃⁻‐N concentrations were greatest in the flowing backwater where groundwater inputs were high. Ambient nitrification in the MISS was twice that in the SACN and tended to be lowest in the main channel. Denitrification was 3× greater in the MISS than that in the SACN, N‐limited in both rivers. Community production/respiration was >1 in the MISS and likely provisioned labile C to fuel microbial metabolism and dissimilatory NO₃⁻‐N reduction, whereas the heterotrophic (production/respiration < 1) nature of the SACN likely limited microbial metabolism and NO₃⁻‐N dissimilation. It appears that N‐cycling in the SACN was driven by groundwater, whereas that in the MISS was supported mainly by water column N‐sources.