Seagrasses are marine angiosperms widely regarded as ecosystem engineers by providing habitat for a variety of species and for their ability to alter sediment biogeochemistry through trapping of suspended sediment, release of oxygen from roots and rhizomes, and excretion of organic carbon from roots and rhizomes. Seagrass ecosystems are threatened by eutrophication tied to coastal development, which results in limited light reaching the benthos, as well as the build-up of toxic porewater sulfide in the sediments underlying the meadow, which has resulted in mass mortality events. In this dissertation, I assess how the dominant seagrass in West Falmouth Harbor, on Cape Cod, MA (Zostera marina, also known as eelgrass), alter their environment at varying stages of degradation, from a formerly-vegetated region over a decade post-mortality of seagrass, to a dense, healthy meadow. This site is a well-studied eutrophic estuary that experienced a large and continuing increase of nitrogen (N) loading since the early part of this century. In chapter 2, I assess patterns of seagrass trapping of sediment and carbon across meadow edges, and find enhanced C accumulation just outside of seagrass meadows. Additionally, I find significant impacts of tropical storms on sediment accumulation, with both enhanced deposition and erosion of sediment, depending on storm intensity. In chapter 3, I assess the role of epiphytic organisms on seagrass leaves in altering seagrass rhizosphere biogeochemistry. I report differences in the relationship between sulfide buildup and light depending on epiphyte presence, and isotopic evidence of the role epiphytic N-fixation plays in maintaining seagrass health in high sulfide environments. In chapter 4, I assess long-term alterations in iron (Fe) mineral speciation following seagrass meadow mortality and high-sulfide. I find evidence of legacy effects of eutrophication and sulfide on formerly-vegetated regions, evidenced by high FeS2 even after soluble sulfide concentrations have returned to healthy values. The altered Fe mineral pool presents an impediment to future restoration efforts, as we found in a follow-up mesocosm experiment, as lower levels of reactive Fe in the sediment may lead to spikes in sulfide concentrations and reduced sediment N-fixation.