River restoration projects focused on increasing flow heterogeneity and channel biodiversity through use of in-channel structures can facilitate ecosystem services which promote nitrogen (N) storage and reduce eutrophication, essential aspects of N dynamics in streams. 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 ranged from 28.0 to 731.7 μg l-1 among all sites, with the highest concentrations occurring at restored sites overall. Average NO3- concentrations ranged from 9.6 to 26.4 mg l-1 but did not differ between restored and unrestored sites (p=0.10). Average NH4+ fluxes at restored sites ranged from -11.5 to 6.5 μg m-2 sec-1, however restoration did not significantly influence NH4+ uptake or regeneration rates between 0-3 minutes and 3-10 minutes. However average NO3- uptake fluxes among sites responded significantly to physical disturbances ranging from -148.8 to 432.6 μg m-2 sec-1. Neither NH4+ nor NO3- fluxes were significantly correlated with chlorophyll-a (Chl-a), total organic matter (TOM) or sediment grain size. We attributed variations in overall N fluxes to N-specific sediment storage capacity, biogeochemical transformations and potential legacy effects associated with urban pollution. It is clear that a greater understanding of mechanisms driving the dynamic transfer, processing, and removal of NH4+ and NO3- in urban river systems is required for informing future river restoration strategies.