Excess nitrogen (N) originating from stormwater runoff in urban areas comes from diffuse sources and is difficult to manage and remediate. One site affected by nonpoint source pollution is Lake Keith, located in Cave Springs, Arkansas, which contains water rich in nitrate-N (5−6 mg N/L). Microdialysis, a diffusion-based sampling technique, has been recognized as a tool for collecting samples from and monitoring chemical changes in soil microsites such as the rhizosphere. Successfully using microdialysis in soil obtained from Lake Keith, an anthropogenically disturbed location that differs in physical and chemical characteristics from the soils studied in past microdialysis studies, will add to the applicability of the sampling technique and promote its establishment as a conventional soil sampling method. In this study, microdialysis was employed to investigate the dynamics of nitrogen in (1) unvegetated soil at different soil saturations and (2) in the rhizosphere of native plant speciesSwitchgrass (Panicum virgatum) and Reed canarygrass (Phalaris arundinacea). Diffusive fluxes in the Switchgrass treatment were either minimal or undetectable, and these data were complemented by the significantly decreased concentrations of nitrate-N and total N in the soil and the accumulation of plant biomass N and total biomass production. On the contrary, the Reed canarygrass treatment consistently exhibited the greatest fluxes of nitrate-N, along with decreased biomass growth. Ultimately, the microdialysis technique differentiated nitrogen dynamics in differing water saturation conditions and in the rhizospheres of two native plants, varying by functional wetland indicator status under the conditions provided by the greenhouse setting.