The rationale of present study was to compare nature of dissolved inorganic nitrogen (DIN = NH4+ and NO2+3) release from aerobic sediment slurry at two different hydrologic flow regimes. The watershed of the Guadalupe River/Estuary system receives more freshwater inflow compared to the watershed of the Nueces River/Estuary system, thus the Nueces Estuary is more saline than the Guadalupe Estuary. Sediment samples were collected using cores, analyzed for organic matter and grain-size, and used to perform laboratory experiments to measure DIN release. During the experiments, DIN concentrations in overlying water were measured for 48 hours in five different salinity treatments. NH4+ concentrations were higher in the Nueces River and Estuary treatments compared to similarly treated samples from the Guadalupe River and Estuary. An increase in NO2+3 concentrations along salinity gradients of the Nueces Estuary treatments indicates favorable condition for nitrification. The Guadalupe River sediments that were not exposed to salinity had an increase in NH4+ concentration at 7.5 ppt. The different DIN release among salinity treatments indicates that hydrologic forcing on organic matter deposition and salinity have an important role on the retention and release of inorganic nitrogen at the sediment-water aerobic layers in rivers and estuaries.