Nuisance and high-tide flooding in coastal zones are increasing due to the combined effects of tidal variability, sea level rise, and non-tidal residuals, such as storm surges and locally generated wave runup. While traditional gray infrastructure, such as seawalls, dikes, and breakwaters, can reduce immediate flood hazards, it often alters coastal hydrodynamics, can amplify tidal ranges, and sometimes transfers risk from one area to another. These limitations have led to growing interest in nature-based “green” approaches, including salt marshes, mangroves, and seagrass, which offer adaptive, self-maintaining protection. However, evaluating the long-term flood-reduction performance of these vegetative systems remains challenging, mainly because of the computational intensity of high-resolution modeling over decadal-to-century timescales. To address this need, we adapt a Hybrid Harmonic Model (HHM) capable of simulating estuarine total water levels at ten-minute resolution over one-hundred-year periods. The HHM integrates 35-day hydrodynamic simulations with harmonic contributions from tides, storm surges, and non-tidal residuals across green, gray, and hybrid adaptation strategies. This approach enables quantification of expected flooding hours, determination of nuisance flooding thresholds, and evaluation of adaptation benefits under future sea level rise. Also, the advantage of the hybrid model’s speed is the ability to efficiently simulate a multitude of stochastic futures to quantify natural variability and generate probabilistic metrics. The model is currently being applied to estuaries along the U S West and Gulf Coasts, representing a range of mixed semidiurnal and diurnal tidal systems, to assess its transferability across diverse environments. By combining process-based and harmonic techniques, HHM provides a computationally efficient tool for informing stakeholder decision-making on climate-resilient estuarine adaptation.