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, while that of less eutrophic tributaries is not (e.g., St Croix River; SACN). We examined components of nitrogen cycling in two 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 highest in flowing habitats in the MISS and often undetectable in isolated backwaters (IBW) except where groundwater inputs occurred. In the SACN, (NO3-N) concentrations were greatest in the flowing backwater (FBW) where groundwater inputs were high. Ambient nitrification in the MISS was 2x that in SACN and tended to be lowest in the main channel (MC). Denitrification was 3x higher in the MISS than SACN; N-limited in both rivers. Community P/R (production/respiration) was >1 in the MISS and likely provisioned labile C to fuel microbial metabolism and dissimilatory NO3-N reduction, while the heterotrophic (P/R<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, while that in the MISS was supported mainly by water column N-sources.