The Sistema Zacatón karst area in northeastern Mexico (Tamaulipas state) is limited to a relatively focused area (20 km2) in a carbonate setting not prone to extensive karstification. The unique features found here are characteristic of hydrothermal karstification processes, represent some of the largest phreatic voids in the world, and are hypothesized to have formed from interaction of a local Pleistocene magmatic event with the regional groundwater system. Aqueous geochemical data collected from five cenotes of Sistema Zacatón between 2000 and 2009 include temperature (spatial, temporal, and depth profiles), geochemical depth profiles, major and trace ion geochemistry, stable and radiogenic isotopes, and dissolved gases. Interpretation of these data indicates four major discoveries: 1) rock-water interaction occurs between groundwater, the limestone matrix, and local volcanic rocks; 2) varying degrees of hydrogeological connection exist among cenotes in the system as observed from geochemical signatures; 3) microbially-mediated geochemical reactions control sulfur and carbon cycling and influence redox geochemistry; and 4) dissolved gases are indicative of a deep volcanic source. Dissolved 87Sr/86Sr isotope ratios (mean 0.70719) are lower than those of the surrounding Cretaceous limestone (0.70730-0.70745), providing evidence of groundwater interaction with volcanic rock, which has a 87Sr/86Sr isotope ratio of 0.7050. Discrete hydraulic barriers between cenotes formed in response to sinkhole formation, hydrothermal travertine precipitation, and shifts in the local water table, creating relatively isolated water bodies. The isolation of the cenotes is reflected in distinct water chemistries among them. This is observed most clearly in the cenote Verde where a water level 4-5 meters lower than the adjacent cenotes is maintained, seasonal water temperature variations occur, thermoclines and chemoclines exist, and the water is oxic at all depths. The surrounding cenotes of El Zacatón, Caracol, and La Pilita show constant water temperatures both in depth profile and in time, have similar water levels, and are almost entirely anoxic. A sulfur (H2S) isotope value of δ34S = -1.8 ‰ (CDT) in deep water of cenote Caracol, contrasted with two lower sulfur isotopic values of sulfide in the water near the surface of the cenote (δ34S = -7 ‰ and -8 ‰ CDT). These δ34S values are characteristic of complex biological sulfur cycling where sulfur oxidation in the photic zone results in oxidation of H2S to colloidal sulfur near the surface in diurnal cycles. This is hypothesized to result from changes in microbial community structure with depth as phototropic, sulfur-oxidizing bacteria become less abundant below 20 m. Unique microbial communities exist in the anoxic, hydrothermal cenotes that strongly mediate sulfur cycling and likely influence mineralization along the walls of these cenotes. Dissolved CO2 gas concentrations ranged from 61-173 mg/L and total dissolved inorganic carbon (DIC) δ13C values measured at cenote surfaces ranged from -10.9 ‰ to -11.8 ‰ (PDB), reflecting mixed sources of carbon from carbonate rock dissolution, biogenic CO2 and possibly dissolved CO2 from volcanic sources. Surface measurements of dissolved helium gas concentrations range from 50 nmol/kg to 213 nmol/kg. These elevated helium concentrations likely indicate existence of a subsurface volcanic source; however, helium isotope data are needed to test this hypothesis. The results of these data reflect a speleogenetic history that is inherently linked to volcanic activity, and support the hypothesis that the extreme karst development of Sistema Zacatón would likely not have progressed without groundwater interaction with the local igneous rocks