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Extreme water-level recurrence estimates for a complex estuary using a high-resolution 2D model and a new method for estimating remotely generated sea level anomalies (SLAs) at the model boundary have been developed. The hydrodynamic model accurately resolves the dominant physical processes contributing to extreme water levels across the Washington State waters of the Salish Sea, including the relative contribution of remote SLA and other non-tidal residual processes that drive extreme water levels above the predicted tide. The model’s predictions have errors of less than 15 cm (<5% of 3–4 m tidal range) at eight tide gauge locations across the model domain. The influence of remote SLAs at the seaward boundary of the model was implemented using a multivariate regression of readily available and locally relevant wind, sea surface temperature, and pressure anomaly data, combined with El Niño Index data (R2 = 0.76). The hydrodynamic model simulations using the remote SLA predictor compared well with simulations using the widely used data-assimilative global ocean model HYCOM SLA data (root mean square difference of 5.5 cm). Extreme water-level recurrence estimates with and without remote SLA show that remote forcing accounts for 50–60% of the total water level anomaly observed along Salish Sea shorelines. The resulting model simulations across decadal timescales provide estimates of extreme water level recurrence across the Salish Sea, capturing climate variability important to long-term coastal hazard planning. This approach has widespread applications for other complex estuarine systems.