<p><strong>Abstract.</strong> Summer cyanobacterial blooms caused an elevation in pH (9 to ~10.5) that lasted for weeks in the shallow and tidal-fresh region of the Sassafras River, a tributary of Chesapeake Bay (USA). Elevated pH promoted desorption of sedimentary inorganic phosphorus and facilitated conversion of ammonium (NH<sub>4</sub><sup>+</sup>) to ammonia (NH<sub>3</sub>). In this study, we investigated pH effects on exchangeable NH<sub>4</sub><sup>+</sup> desorption, pore water diffusion and the flux rates of NH<sub>4</sub><sup>+</sup>, soluble reactive phosphorus (SRP) and nitrate (NO<sub>3</sub><sup>&minus;</sup>), nitrification, denitrification, and oxygen consumption. Elevated pH enhanced desorption of exchangeable NH<sub>4</sub><sup>+</sup> through NH<sub>3</sub> formation from both pore water and adsorbed NH<sub>4</sub><sup>+</sup> pools. Progressive penetration of high pH from the overlying water into sediment promoted the mobility of SRP and the release of total ammonium (NH<sub>4</sub><sup>+</sup> and NH<sub>3</sub>) into the pore water. At elevated pH levels, high sediment-water effluxes of SRP and total ammonium were associated with reduction of nitrification, denitrification and oxygen consumption rates. Alkaline pH and the toxicity of NH<sub>3</sub> may inhibit nitrification in the thin aerobic zone, simultaneously constraining coupled nitrification–denitrification with limited NO<sub>3</sub><sup>&minus;</sup> supply and high pH penetration into the anaerobic zone. Geochemical feedbacks to pH elevation, such as enhancement of dissolved nutrient effluxes and reduction in N<sub>2</sub> loss via denitrification, may enhance the persistence of cyanobacterial blooms in shallow water ecosystems.</p>