The increasing frequency of extreme rainfall is leading to a rise in groundwater levels in coastal areas, significantly affecting high-speed railway operations. To address this concern, this study developed a 2.5-dimensional finite element model of a coupled track-embankment-ground system based on Biot’s porous media theory to analyze the effect of groundwater level rise on the critical velocity of high-speed railways and vibration responses. The findings reveal a consistent decrease in the critical velocity of high-speed railways with rising groundwater levels. Particularly, the increase in groundwater levels within the embankment significantly influences the critical velocity compared to a similar rise in the foundation’s groundwater level. Furthermore, deformations induced by passing trains significantly increase as groundwater levels rise. Specifically, when the groundwater level rises from the foundation bottom to the subgrade surface, subgrade surface deformation increases by approximately 55%. As trains approach the critical velocity, significant vibration phenomena, known as the “Mach effect,” occur at the foundation surface. Importantly, as groundwater levels rise, the “Mach effect” intensifies. Analyzing the vibrating frequency spectrum of the displacement response demonstrates a substantial increase in vibration amplitude, particularly in the high-frequency region, as groundwater levels rise. This study highlights that the rise in groundwater level not only amplifies vibrations but also extends the propagation of high-frequency vibrations, underscoring the importance of effective embankment waterproofing in controlling track vibrations.