Floodplains exert important controls on water and nutrient processing, yet spatial heterogeneities in floodplain characteristics result in variable effectiveness. In this study, we evaluated the spatial relations among topographic, lithologic and water quality features within the Cedar River floodplain located in southeastern Iowa. Floodplain topography and lithology were dominated by a series of sandy ridges and fine-textured swales typical of a natural meandering river floodplain complex. Groundwater sampling results from 10 monitoring wells placed in representative ridge and swale environments indicated that water quality varied systematically. Beneath sand-dominated ridges, water was aerobic and had low specific conductance, and higher concentration of NO3–N and lower concentrations of PO4–P and dissolved organic carbon (DOC). Groundwater beneath swales was anaerobic and typified by high specific conductance, and higher concentrations of NH4–N, PO4–P and DOC. We extrapolated the results from point measurements to the entire floodplain area using surface geophysics and light detection and ranging using co-kriging to map the distribution of groundwater geochemical environments at the study site. Results are seen to provide an approach to better predict shallow groundwater quality in large river floodplains and improve our ability to manage ecosystem services in these strategic locations. Copyright © 2011 John Wiley & Sons, Ltd.