The concentration and form of dissolved organic C (DOC) and N species (NH4+ and NO3-) were investigated as part of a larger hydrogeochemical study of the Cottonwood Lake Study Area within the Prairie Potholes region. Groundwater, pore water and surface wetland water data were used to help characterize the relationships between surface and groundwater with respect to nutrient dynamics. Photosynthesis and subsequent decomposition of vegetation in these hydrologically dynamic wetlands generates a large amount of dissolved C and N, although the subsurface till, derived in part from organic matter rich Pierre Shale, is a likely secondary source of nutrients in deeper groundwater. While surface water DOC concentrations ranged from 2.2 to 4.6 mM, groundwater values were 0.15 mM to 3.7 mM. Greater specific UV absorbance (SUVA254) in the wetland water column and in soil pore waters relative to groundwater indicate more reactive DOC in the surface to near-surface waters. Circumneutral wetlands had greater SUVA254, possibly because of variations in vegetation communities. The dominant inorganic nitrogen species was NH4+ in both wetland water and most ground water samples. The exceptions were 3 wells with NO3- ranging from 38 to 115 μM. Shallow groundwater wells (Well 28 and Well 13S) with greater connection to wetland surface water had greater NH4+ concentrations (1.1 mM and 120 μM) than other well samples (3–90 μM). Pore water nutrient chemistry was more similar to surface water than ground water. Nitrogen results suggest reducing conditions in both groundwater and surface water, possibly due to the microbial uptake of O2 by decaying vegetation in the wetland water column, labile organic C available in shallow groundwater, or the oxidation of pyrite associated with the subsurface.