Amidst a changing climate that has resulted in more intense storm activity and a migration of tropical cyclones towards coastal areas, their full impact on coastal aquifers remains unexplored as of yet. As such, this research examined the effects of tropical cyclones on coastal aquifers, which are often anchialine in nature (i.e., a meteoric freshwater mass overlies a denser saline water mass below) to determine if heightened storm activity results in mixing of the two water masses, thereby increasing the salinity of the meteoric water mass and negatively affecting the potability of coastal aquifers. This was done using diatom microfossils, which are very sensitive to changes in water quality, that were collected from sediment samples in the Yax Chen cave system in the Yucatan Peninsula of Mexico, which experienced two tropical cyclones in 2013 (Ingrid and Manuel). The results of the analysis showed a marked increase in the diatom species Paralia sulcata after 2013, which is a species associated with vertical mixing zones, as well as an increase in Thalassiosira weisflogii, which is a species associated with higher salinity conditions; these results indicate there was indeed increased mixing of the two water masses after the tropical cyclones that resulted in increased salinity of the meteoric water mass.