River restoration projects focused on altering flow regimes through use of in-channel structures can facilitate ecosystem services, such as promoting nitrogen (N) storage to reduce eutrophication. In this study we use small flux chambers to examine ammonium (NH4+) and nitrate (NO3-) cycling across the sediment-water interface. Paired restored and unrestored study sites in 5 urban tributaries of the River Thames in Greater London were used to examine N dynamics following physical disturbances (0-3 min exposures) and subsequent biogeochemical activity (3-10 min exposures). Average ambient NH4+ concentrations were significantly different amongst all sites and ranged from 28.0 to 731.7 μg L-1, with the highest concentrations measured at restored sites. Average NO3- concentrations ranged from 9.6 to 26.4 mg L-1, but did not significantly differ between restored and unrestored sites. Average NH4+ fluxes at restored sites ranged from -8.9 to 5.0 μg N m-2 sec-1, however restoration did not significantly influence NH4+ uptake or regeneration (i.e., a measure of release to surface water) between 0-3 minutes and 3-10 minutes. Further, average NO3- fluxes amongst sites responded significantly between 0-3 minutes ranging from -33.6 to 97.7 μg N m-2 sec-1. Neither NH4+ nor NO3- fluxes correlated to sediment chlorophyll-a, total organic matter, or grain size. We attributed variations in overall N fluxes to N-specific sediment storage capacity, biogeochemical transformations, potential legacy effects associated with urban pollution, and variations in river-specific restoration actions.