We monitored submarine groundwater discharge (SGD) into the Werribee Estuary, Australia, using both chemical and physical methods. SGD occurred at hotspots where 222 Rn persisted through a 12 month survey period. A significant correlation between 222 Rn and NO 3 - (r 2 = 0.8, p < 0.01), as well as between 222 Rn NO 3 - and N 2 O (r 2 = 0.6, p < 0.01) at a 222 Rn NO 3 - hotspot, and much higher and N 2 O concentrations in groundwater relative to surface water suggest that elevated and N 2 O concentrations in the estuary were derived from SGD. Two sampling campaigns over 24 h revealed that variations of 222 Rn, and N 2 O were controlled by tide-induced hydraulic-head gradient fluctuations and, possibly to a much lesser extent, by tidal pumping and density-driven convection. A two-box 222 Rn mass-balance model was used to calculate the rate of SGD into two different layers across the pycnocline of the estuary. A higher total groundwater discharge rate of 0.12 ± 0.09 m d -1 was observed in the surface layer during ebb tide compared with 0.10 ± 0.08 m d -1 during flood tide. Fluxes of groundwater-derived and N 2 O were higher than the riverine flux at baseflow by more than 30 fold and 20 fold, respectively. SGD derived fluxes exceeded the mean annual riverine NO 3 - and TN fluxes by a factor of ~ 5 and ~ 3 respectively. SGD-derived N 2 O fluxes were 170 μmol m -2 d -1 , which are among the highest N 2 O fluxes observed in estuaries.