We examined the effects of seasonal salinity changes on sediment ammonium (NH₄ ⁺) adsorption and exchange across the sediment–water interface in the Parker River Estuary, by means of seasonal field sampling, laboratory adsorption experiments, and modeling. The fraction of dissolved NH₄ ⁺ relative to adsorbed NH₄ ⁺ in oligohaline sediments rose significantly with increased pore water salinity over the season. Laboratory experiments demonstrated that small (∼3) increases in salinity from freshwater conditions had the greatest effect on NH₄ ⁺ adsorption by reducing the exchangeable pool from 69% to 14% of the total NH₄ ⁺ in the upper estuary sediments that experience large (0–20) seasonal salinity shifts. NH₄ ⁺ dynamics did not appear to be significantly affected by salinity in sediments of the lower estuary where salinities under 10 were not measured. We further assessed the importance of salinity-mediated desorption by constructing a simple mechanistic numerical model for pore water chloride and NH₄ ⁺ diffusion for sediments of the upper estuary. The model predicted pore water salinity and NH₄ ⁺ profiles that fit measured profiles very well and described a seasonal pattern of NH₄ ⁺ flux from the sediment that was significantly affected by salinity. The model demonstrated that changes in salinity on several timescales (tidally, seasonally, and annually) can significantly alter the magnitude and timing of NH₄ ⁺ release from the sediments. Salinity-mediated desorption and fluxes of NH₄ ⁺ from sediments in the upper estuary can be of similar magnitude to rates of organic nitrogen mineralization and may therefore be important in supporting estuarine productivity when watershed inputs of N are low.