Karstic wetlands provide important ecosystem services such as maintenance of hydrological balance, flood regulation, drinking water supply and nutrients cycling. It is important to conserve and maintain karstic wetlands due to its interaction with groundwater systems and its socioeconomic relevance. The objective of this research was to generate base-line knowledge of the microtopography, hydroperiod and biogeochemical characteristics of poorly known tropical karstic marshes by testing two hypotheses, the phreatotrophic nature of tropical karstic marshes, and the alteration of its biogeochemistry by a highway dividing the marsh. The study site is located in the north of the state of Quintana Roo (Mexico), in pseudo-paludal depressions associated to fractures. The water level varied from few centimeters below the ground to more than 100 cm. We demonstrate that the wetland is groundwater-fed with differences among groundwater, interstitial and surface water in almost all parameters measured. The water is calcium bicarbonate type; the main processes occurring are recharge, evaporation and rock dissolution. Our results suggests active denitrification, low phosphates attributed to Ca- and Fe/Al-bound P, elevated alkalinity and sulfate reduction due to anaerobic conditions in water and soil. The soil reflect its sedimentary origin, the bulk density is low with very high water retention capacity. We do not have enough evidence of the highway modifying the biogeochemistry or hydrology of the marsh. These karstic wetlands provide important provisioning and supporting ecosystem services that should be studied, acknowledged and maintained.