The water level forecasting system represented by the hydrodynamic model relies too much on the input data and the forecast value of the boundary, therefore introducing uncertainty in the prediction results. Tide tables ignore the effect of the residual water level, which is usually significant. Therefore, to solve this problem, a water level forecasting method for the regional short-term (3 h) is proposed in this study. First, a simplified MIKE21 flow model (FM) was established to construct the regional major astronomical tides after subdividing the model residuals into stationary constituents (surplus astronomical tides, simulation deviation) and nonstationary constituents (residual water level). Harmonic analysis (HA) and long short-term memory (LSTM) were adopted to forecast these model residuals, respectively. Finally, according to different spatial background information, the prediction for each composition was corrected by the inverse distance weighting (IDW) algorithm and its improved IDW interpolation algorithm based on signal energy and the spatial distance (IDWSE) from adjacent observation stations to nonmeasured locations. The developed method was applied to Narragansett Bay in Rhode Island. Compared with the assimilation model, the root-mean-square error (RMSE) of the proposed method decreased from 12.3 to 5.0 cm, and R² increased from 0.932 to 0.988. The possibility of adding meteorological features into the LSTM network was further explored as an extension of the prediction of the residual water level. The results show that the accuracy was limited to a moderate level, which is related to the difficulty presented by using only wind features to completely characterize the regional dynamic energy equilibrium process.