Periodic oscillations between El Niño and La Niña conditions in the Pacific Basin affect oceanographic and meteorological phenomena globally, with impacts on the abundance and distribution of marine species. However, El Niño effects on estuarine hydrology and tidal wetland processes have seldom been examined rigorously. We used detailed wetland elevation and local inundation data from 10 tidal wetlands located along the Pacific coast of the United States to assess changes in flooding during the 2015–2016 El Niño and to determine decadal‐scale relationships between estuarine sea‐level anomalies and Pacific Basin climate indices for this region. During the 2015–2016 El Niño all sites experienced significant increases in high‐tide water levels exceeding those predicted by astronomical tides, and increased flooding frequency during at least one of the El Niño subperiods relative to pre‐El Niño conditions. The magnitude of positive sea‐level anomalies varied by site (4–15 cm), with local hot spots of high water in southern Oregon, northern California, and Pt. Mugu lagoon in the Southern California Bight. Furthermore, over the last three decades of historic tide records, there were positive relationships between high‐tide sea‐level anomalies and equatorial Pacific Basin sea surface temperature anomalies across the region, and negative relationships with the Northern Oscillation Index. Increases of 1 °C in equatorial sea surface temperature were associated with 3–5 cm of increased high‐tide flooding at the sites. Elevated estuarine flooding associated with future El Niños could impact important tidal wetland processes and could be an additive stressor for wetlands facing accelerating sea‐level rise.