Accurate and timely water level predictions are essential for effective shoreline and coastal ecosystem management. As sea levels rise, the frequency and severity of coastal inundation events are increasing, causing significant societal and economic impacts. Predicting these events with sufficient lead time is essential for decision-makers to mitigate economic losses and protect coastal communities. While machine learning methods have been developed to predict water levels at specific sites, there remains a need for more generalized models that perform well across diverse locations. This study presents a robust deep learning model for predicting water levels at multiple tide gauge locations along the Gulf of Mexico, including the open coast, embayments, and ship channels, all near major ports. The selected architecture, Seq2Seq, achieves significant improvements over the existing literature. It meets the National Oceanic and Atmospheric Administration’s (NOAA) operational criterion, with the percentage of predictions within 15 cm for lead times up to 108 h at the tide gauges of Port Isabel (92.2%) and Rockport (90.4%). These results represent a significant advancement over current models typically failing to meet NOAA’s standard beyond 48 h. This highlights the potential of deep learning models to improve water level predictions, offering crucial support for coastal management and flood mitigation.