The Yalahau region, located in the northeastern portion of the Yucatán Peninsula, hosts a series of elongated depressions trending north/south in the direction of Isla Holbox, identified as the Holbox Fracture Zone. Previous studies have explored the geomorphology and various hydrologic characteristics of the Yucatán Peninsula; however, there is a paucity of data concerning the interior region where the fractures are located. Strontium isotope ratios and major ion geochemistry data of the surface water and groundwater of this region serve as a hydrogeochemical fingerprint, aiding in constraining the hydrological boundaries, determining flow paths, and characterizing hydrogeochemical processes that impact the composition of the groundwater within the region. 87Sr/86Sr isotope ratios indicate a different signature than the surrounding bedrock Sr ratio, suggesting that the flow throughout the Yalahau region is moving through channels faster than that of much of the Yucatán. Through major ion geochemistry and 87Sr/86Sr isotope ratios, we were able to delineate at least two flow paths within the Yalahau region and identify a point of saline intrusion at least 35 km from the coast. Gaining an understanding of the hydrogeochemistry and water flow regions is crucial in determining the impact of various activities (e.g., extensive tourism, drinking water withdrawal, wastewater discharge/injection) that occur within the Yucatán Peninsula.