The magnitude of tidal energy depends on changes in ocean water levels, and by accurately predicting water level changes, tidal power plants can be effectively helped to plan and optimize the timing of power generation to maximize energy harvesting efficiency. The time-dependent nature of water level changes results in water level data being of the time-series type and is essential for both short- and long-term forecasting. Real-time water level information is essential for studying tidal power, and the National Oceanic and Atmospheric Administration (NOAA) has real-time water level information, making the NOAA data useful for such studies. In this paper, long short-term memory (LSTM) and its variants, stack long short-term memory (StackLSTM) and bi-directional long short-term memory (BiLSTM), are used to predict water levels at three sites and compared with classical machine learning algorithms, e.g., support vector machine (SVM), random forest (RF), extreme gradient boosting (XGBoost), and light gradient boosting machine (LightGBM). This study aims to investigate the effects of wind speed (WS), wind direction (WD), gusts (WG), air temperature (AT), and atmospheric pressure (Baro) on predicting hourly water levels (WL). The results show that the highest coefficient of determination (R2) was obtained at all meteorological factors when used as inputs, except at the La Jolla site. (Burlington station (R2) = 0.721, Kahului station (R2) = 0.852). In the final part of this article, the complete ensemble empirical mode decomposition adaptive noise (CEEMDAN) algorithm was introduced into various models, and the results showed a significant improvement in predicting water levels at each site. Among them, the CEEMDAN-BiLSTM algorithm performed the best, with an average RMSE of 0.0759 mh−1 for the prediction of three sites. This indicates that applying the CEEMDAN algorithm to deep learning has a more stable predictive performance for water level forecasting in different regions.