Anthropogenic activity has resulted in increased flows of nitrogen (N) and phosphorus (P) to the coastal zone, resulting in degradation of coastal ecosystems world-wide. In this dissertation, I synthesize twenty years of data collected in West Falmouth Harbor (WFH), a shallow lagoon on Cape Cod, MA, USA that has experienced a marked increase in N load starting in the late 1990s due to input from an aquifer contaminated by a municipal wastewater treatment facility, with no concomitant increase in P load. Nitrogen is the nutrient most often considered as limiting to production in estuarine systems, and it is crucial to accurately characterize the inputs, fluxes, and retention of N within a system to best manage and mitigate eutrophication. I first evaluate spatial and temporal patterns in the N load to WFH over time from 1985 through 2024 using field data collected from wintertime open-water sampling along transects from shore and from groundwater wells, as well as published literature estimates of direct deposition onto surface waters and the diffuse watershed load. For the years when loading was highest (2008-2013), the total N input averaged 3.1 mmol N m-2 d-1 and decreased by 25% by 2024. Wastewater-source N was always the dominant component of the N load.Next, I examine the concentrations of inorganic and total N and P in WFH as well as the exchange with the adjacent coastal ocean. There has been a significant decrease in both inorganic and total N and P concentrations in water entering WFH from the coastal ocean over the period of the study, likely due to changes in ocean circulation and temperature. Coastal waters entering WFH are high in P relative to N when compared to the needs of primary producers. This import of P from coastal waters helps maintain N limitation despite high N input from the contaminated aquifer. Approximately 75% of inorganic N inputs from all sources are retained within the system during the summertime. In contrast, retention of total N is small, 15% in 2005-2009 falling to only 3% in 2014-2019. Net exchange of both inorganic and total P is very small and shows no significant change over time. Gross primary production (GPP) in WFH during the summer months declined by approximately 10% from 2011 through 2023, likely due to the 25% reduction in N load over this time. GPP was higher at the station closest to input from the N-contaminated groundwater source. Inorganic P was consistently lower at this site, strongly supporting that N and not P limits primary production in WFH. There was high day-to-day variability in metabolic rates, which can be partially explained by variations in solar radiation and water temperature. GPP and ecosystem respiration were tightly coupled, suggesting that much of the daily respiration is by the autotrophs themselves. Net ecosystem production each year was less than 0.1 mmol O2 m_2 d_1, and shifted in pattern from net heterotrophy in 2005-2009 to net autotrophy beginning in 2010.