Natural cave passages penetrating coastal aquifers in the Yucatan Peninsula (Quintana Roo, Mexico) were accessed to investigate how regional meteorology and hydrology control dissolved organic carbon and methane dynamics in karst subterranean estuaries, the region of aquifers where fresh and saline waters mix. Three field trips were carried out in December 2013, August 2014, and January 2015 to obtain 1) physicochemical and 2) geochemical data from the water column and 3) temporal records of water chemistry and hydrological parameters below and above the surface at three sites within the Ox Bel Ha cave (Cenote Jailhouse, Cenote Naach Wennen Ha, and Cenote Odyssey) and another cave (Cenote Crustacea). These efforts resulted in vertical physicochemical and geochemical profiles from the water column of the flooded caves from the region. In addition, the sampling resulted in temporal chemical and hydrological records of dissolved methane concentrations and chloride concentrations (used to calculate salinity) from August 2014 to January 2015, sampled by OsmoSamplers. The records encompass wet and dry seasons and include the impact of Tropical Storm Hanna during October 2014. Field activities were carried out by the U.S. Geological Survey (USGS) Coastal and Marine Geology Program in conjunction with Texas AM University at Galveston.