Gao, YonghuiNutrient supply, including `new' nitrogen (N) added through N₂-fixation, nutrient release from sediments and freshwater inflow, can be important in increasing and sustaining estuarine phytoplankton blooms. In return, dense blooms in shallow water estuaries may affect nutrient recycling by elevating the pH and dissolved oxygen (DO) concentrations as well as increasing sedimentation of phytoplankton detritus. My dissertation addressed the interaction between cyanobacterial blooms and biogeochemical nutrient recycling in the tidal-fresh and oligohaline region of the Sassafras River, a tributary of the Chesapeake Bay, Maryland, USA. When high pH overlying water comes in contact with sediments, the subsequent pH penetration causes desorption of exchangeable ammonium and converts NH₄ <super>+</super> to NH₃ from both porewater and absorbed NH₄ <super>+</super> pools. Alkaline pH and the toxicity of NH₃ may inhibit nitrification in the thin aerobic zone. During massive cyanobacterial blooms in summer, high effluxes of SRP and total ammonium from sediments were associated with reduced nitrification and denitrification rates. Retention of N in the upper estuary and increased dissolved inorganic nitrogen (DIN) release into the water column may facilitate nitrogen assimilation by cyanobacteria in N-limited water. High pH also resulted in a significant increase in soluble reactive phosphate (SRP) flux and lead to relatively high SRP compared to DIN flux rates, which may support the high P demand of diazotrophic cyanobacteria. As N became limiting in summer, the dominant cyanobacterial assemblage changed from non-N₂ fixers (Microcystis spp.) to N2 fixers (<italic>Anabaena </italic> spp., <italic>Pseudanabaena </italic> sp. and <italic>Synechococcus </italic> sp.). Warm temperatures, high P availability and low salinity are environmental factors associated with high rates of N2 fixation. Dissolved inorganic carbon (DIC) limitation, high pH, and high DO concentrations, mediated by cyanobacterial photosynthesis, can cause decreases in photosynthetic efficiency and daytime N₂ fixation of the cyanobacterial assemblage. Species succession appears to enable the cyanobacterial assemblage to adapt to changing environmental conditions caused by the bloom, including high pH and DO, and to maintain N₂ fixation for sustained growth.DissertationEnvironmental scienceBiogeochemistryBiological oceanographyCoupled nitrification-denitrificationCyanobacterial bloomsNitrogen fixationnutrient flux at the sediment-water interfaceNutrient inputpH and dissolved oxygen