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Management efforts to reduce nutrient pollution have prompted the recovery of submersed aquatic vegetation (SAV) in the Chesapeake Bay (CB), particularly in the Bay’s tidal fresh and oligohaline waters. Unfortunately, benthic filamentous cyanobacteria have also become increasingly common in some of the areas where SAV is expanding the most. Although the prevalence of cyanobacteria is increasing globally, it is relatively uninvestigated in CB where it may threaten the stability and resilience of recovering SAV, disrupt the nutrient balance of SAV beds, which are generally thought to be nutrient sinks, and potentially affect recreational and commercial activities if they produce toxic compounds. The proposed research broadly aims to better understand the causes and effects of increasing benthic cyanobacteria abundance in CB. Our objectives are to 1) determine what conditions support cyanobacteria growth by conducting field surveys of cyanobacteria distribution in relation to SAV biomass and environmental variables in the upper CB and several oligohaline tidal tributaries 2) determine the effects of environmental variables (nutrients, light) on cyanobacteria production, nutrient uptake, nitrogen fixation, and potential toxin production by conducting bio-assay experiments, 3) assess the effects of cyanobacteria on biogeochemical rate processes and SAV via nutrient flux experiments and ecological simulation modeling exercises, and 4) determine whether toxins are present in cyanobacteria tissue and the water column through chemical analysis. We anticipate that our results will generate important scientific insights about the role of benthic cyanobacteria in shallow, oligohaline ecosystem recovery dynamics. These insights will also inform management efforts aimed at protecting human and ecological health in CB.