Beaver ponds, once absent from many watersheds due to extirpation of beaver, are now reemerging in more urbanized landscapes, where they increasingly interact with anthropogenic pollutants such as nitrate. Beaver ponds play a disproportionate role in biogeochemical cycling and greenhouse gas (GHG) emissions, raising questions about their net impact on climate feedbacks. This study examines how nitrogen enrichment alters microbial community dynamics, nutrient cycling, and GHG fluxes in beaver ponds, offering novel insights into their ecological and climatic implications. This study used a multi-season in situ mesocosm experiment (Fall 2023, Spring 2024, Summer 2024) to explore how nitrate additions impact metabolism, and GHG production. Fall 2023 results revealed a sharp rise in nitrous oxide emissions under nitrogen enrichment, substantially increasing global warming potential (GWP). Conversely, Spring and Summer trials indicated reduced methane emissions in treatment plots, potentially offsetting nitrous oxide increases and leading to a lower net GWP. These findings suggest nitrate enrichment interacts with seasonal variability to modulate microbial processes such as methanogenesis and denitrification, underscoring the complexity of nutrient pollution’s effects. Beyond traditional metrics, microbial data collected from the water column and sediment surface enables for assessments of the microbial community that is potentially driving observed biogeochemical changes. Coupled with detailed metabolic measurements—including oxygen production/consumption, photosynthetically active radiation, and nutrient uptake—the research captures a comprehensive picture of system-wide metabolism and its response to nitrate enrichment. These findings advance our understanding of nutrient pollution’s multifaceted effects on small freshwater systems and highlight the multifaceted role of beaver ponds as nitrate attenuators, and their variable role in GHG emission.