The primary clientele of a harbor is vessels, and vessels are primarily influenced by external forces such as wind (on the water surface), currents (underwater), and waves (affecting vessel stability). Therefore, it is necessary to comprehensively consider safety factors such as marine environmental forces and port characteristics. As ship sailing falls under applied science, acquiring marine meteorological information regarding ship routes can enhance port navigational safety. However, in the face of changes in the environmental conditions of harbor waters, it is essential to fully consider the impact of the external environment on ship maneuvering. One can effectively navigate complex operating environments by devising reasonable ship-handling plans. In the context of sea level rise caused by extreme climatic events, long-term variations, trends, and random factors are at play. Previous assessments of sea level rise have often relied on linear regression and the least squares method to determine coefficients. However, these methods fail to accurately capture the actual trend of sea level rise. Additionally, traditional harmonic analysis methods are unable to analyze sea level rise as well. Therefore, in this study, the techniques of simple moving average (SMA), empirical mode decomposition (EMD), and ensemble empirical mode decomposition (EEMD) were applied to analyze sea level rise. The obtained results of sea level rise under different analysis conditions were integrated with a hydrodynamic model that incorporates both wave and tidal characteristics to calculate the overall coastal dynamics parameters, which are crucial for ship navigation. The research findings contribute to the study of ship navigational safety issues by examining the distribution characteristics of port meteorology under climate change conditions. They offer valuable insights for mariners to assess navigational safety and devise maneuvering strategies based on the actual water flow conditions. Furthermore, the findings help identify and address potential risks and issues, ultimately ensuring the safety of navigation.