Increased organic matter inputs in eutrophic marine coastal systems may lead to high levels of microbial sulfate reduction and elevated concentrations of sulfide in porewaters, resulting in subsequent declines in seagrass health. I examined this process in West Falmouth Harbor, a nitrogen (N)- enriched lagoon in Cape Cod. West Falmouth Harbor can be divided into three sub-basins: Snug Harbor, which is impacted by N-inputs from groundwater and contained seagrass until a die-off event in 2010; the Middle Harbor, which is impacted by N-enrichment and contains seagrass; and the Outer Harbor, which contains a seagrass meadow but is less N-impacted. I found the highest levels of porewater sulfide in the Middle Harbor, with an average rooting zone value of 2.3 mM total soluble sulfide, as well as sediment organic matter values as high as 15%, and average δ34S leaf tissue value of 0.0 ‰, implying plant exposure to isotopically light porewater sulfides. This contrasts with much lower sulfide and sediment organic matter concentrations in the Outer and Snug Harbors, at 1.0 and 0.7 mM for sulfide, and 6% and 8% organic matter, respectively. Soluble sulfide and δ34S values found in 2007 in the innermost, highly eutrophic Snug Harbor sub-basin prior to the seagrass die-off event in 2010 were comparable to 2018 Middle Harbor values, with soluble sulfides at 3.0 mM and leaf tissue δ34S at 0.2 ‰. Additionally, carbon values have decreased in Snug Harbor, from 4.4% in 2010 to 3.6% in 2018. I found indications of poor seagrass health in the Middle Harbor, including belowground biomass averaging 64 g per m2, compared to 106 g per m2 in the Outer Harbor. The Middle Harbor had a normalized difference vegetation index value nearly 2-fold higher than the Outer Harbor, indicating potential light limitation which would decrease seagrass photosynthesis and make them vulnerable to sulfide intrusion. A considerable amount of the light limitation experienced by seagrass in West Falmouth Harbor may result from epiphyte cover, with up to 0.55 mg epiphyte per cm2 seagrass leaf area in both the Middle and Outer Harbors. My study suggests a feedback cycle in West Falmouth Harbor wherein sediment trapping of organic matter in N-enriched, light-limited conditions may highly stress seagrass’s rhizome and root structure, leading to increased susceptibility to other environmental stressors and eventual mortality.