In the Caribbean, coral reefs face unprecedented challenges, with the Stony Coral Tissue Loss Disease (SCTLD) emerging as a predominant threat since 2014. This disease, exacerbated by factors such as extreme bleaching events, hurricane-induced physical damage, and coastal pollution, has led to substantial declines in Caribbean coral populations. Despite extensive conservation efforts, SCTLD has become endemic to the region. Our research delves into the dynamics of the disease propagation in the northern US Virgin Islands reefs. Employing a 2D multi-scale high-resolution biophysical model coupled with an SIR epidemic model, we compare the modeled pattern of transmission with the observed pattern resulting from the continuous monitoring of shallow coral populations in the area in 2019 and 2020. Our study sheds light on the dynamics of the disease at a regional scale and supports the hypothesis of water-borne transmission. This comprehensive modeling approach enhances our understanding of SCTLD dynamics and aids in pinpointing reefs where protection efforts should be concentrated to effectively mitigate the emergence of future outbreaks. Given the looming threat of SCTLD spreading to the Pacific, our findings could guide strategic monitoring/treatment planning and prioritize reef protection initiatives.