Amid mounting concerns about climate change’s impact on coastal areas, this study investigates storm surge dynamics induced by Tropical Depression 29W (TD 29W) using the MIKE 21 model. Comprehending the complex mechanisms behind storm surges is crucial considering gaps in understanding their combined influences, including tide–surge interactions, varying typhoon parameters, and changing storm tracks. The impacts of climate change, including accelerating sea level rise and its correlation with storm surge magnitudes, require detailed investigations for effective disaster management in vulnerable coastal communities. Through precise calibration, matching simulations with tidal gauge stations, this research uncovers the intricate interplay between landfall timing, diverse storm tracks, wind intensities, and the amplifying impact of rising sea levels. Findings indicate surge residuals ranging from −0.03m to 0.01m during TD 29W’s landfall, with higher surge residuals during rising tide phases. Moreover, an increase in TD 29W’s maximum wind speed moderately influences positive surges while significantly amplifying negative surge heights by 68% to 92% with wind speed increments. An analysis of typhoon track variations emphasizes the vulnerability of the Pahang coast to changing storm dynamics, underlining the need for tailored resilience strategies. Projections suggest a significant surge height increase by the year 2100, emphasizing the urgency of adaptive measures for the region.