Estuaries and coastal waters are sensitive to ecological degradation but receive some of the highest levels of pollutants. One impact of these pollutants is increased greenhouse gas generation, which is significant, but difficult to estimate due to high variability and data paucity. This paper investigates key controls on methane (CH4) and nitrous oxide (N2O) in the urban, mesotidal, stratified Clyde estuary, Scotland, between January 2020 and October 2022. Measurements covered the estuary longitudinally, through tidal cycles and across the river-estuary transition. Dissolved CH4 and N2O were always supersaturated relative to air exhibiting strong spatial and temporal variability. Estuary surface freshwater layer CH4 concentrations were positively correlated with turbidity and exceeded 5.4 μmol l−1. Lower saline layer CH4 concentrations exceeded 10.8 μmol l−1 and were highest after freshwater flushing events. The CH4 concentrations decreased exponentially with salinity persistence (time since last freshwater flushing event), reducing by 50% after 10 days of continuously saline water. Salinity persistence likely provides a tipping point between the dominance of different microbial communities. Considering the persistence of saline conditions can explain much of the previously reported variability in estuarine CH4. In the surface freshwater layer, N2O exceeded 0.15 μmol l−1, while in the lower saline layer N2O exceeded 0.21 μmol l−1, despite lower dissolved nitrogen, increasing the N2O per unit available nitrogen. There was a significant inverse exponential correlation (R2 = 0.96) between N2O and dissolved oxygen in the lower layer, with low oxygen driving elevated N2O concentrations. This study provides unique insights into the conditions that generate CH4 and N2O in a stratified urban-impacted estuary.