Anthropogenic nutrient loading into freshwater systems can have significant impacts on ecosystem function. However, the effect of stoichiometric imbalances of nitrogen (N) and phosphorus (P) on microbial communities and associated biogeochemical processes remains poorly studied. We assessed the impact of stoichiometric extremes on the sediment-water interface during a fertilization experiment conducted in twelve limnocorrals located in three ponds at the University of Mississippi Field Station in (Abbeville, MS). During the sampling seasons of 2019, 2020, and 2021, the limnocorrals were fertilized to target N:P (molar) ratios of 2.2, 16, 55, and 110. These open-bottomed mesocosms allowed for biogeochemical exchange with the sediments. In August of 2021, sediment cores were collected from each limnocorral and the surrounding ponds. Sediment cores were used in a flow through incubation experiment to measure N2 flux in the sediment water interface. Following the intact core experiment, the first centimeter of sediment was analyzed for total N, C, and P. DNA was also extracted and whole genome metagenomic sequencing was performed. N2 flux data suggested that net N fixation occurred at the sediment water interface of the 2.2 and 16 N:P treatments but net denitrification occurred in the 55 and 110 N:P treatments. There were negligible differences in the N, C, and P in the first cm of sediment between the treatments, but the treated limnocorral sediments were more P rich than the control sediment. There were also no significant differences in the functional potential of the microbial communities between the treatments or the ponds. Despite similar physiochemical properties and microbial functional potential, there were some significant differences in microbial community structure. The 2.2 N:P treatment had significantly more diazotrophic cyanobacteria genera compared to the 110 N:P treatment, while the 110 treatment had significantly more genera known for iron oxidation compared to the 2.2 treatment.