Increasing atmospheric CO2 concentrations have intensified processes such as the acidification of aquatic ecosystems, where wetlands, despite their climate vulnerability, play a crucial role as carbon sinks. To characterize the spatiotemporal dynamics of the carbon system in the El Hato wetland, monthly sampling was conducted between January and December 2015 at five stations and two depth strata. Physical, chemical, and biological parameters were measured, and the components of the carbon system were calculated using the CO2SYS program based on pH and total alkalinity. Statistical analyses included nonparametric tests, Spearman correlations, and multivariate analysis. The results showed significant variation in total alkalinity (406.29-1650.62 μmol/l) and total inorganic carbon (268.49-1948.58 μmol/l), with maxima during the rainy season and minima during the dry season. The pH ranged unusually wide (5.6-11.2), associated with both karst lithology and autotrophic metabolism. Undersaturated conditions of calcite and aragonite (Ω<1) predominated, with a brief episode of supersaturation in August. Furthermore, vertical differences in fCO2 and acidification events linked to bacterial respiration and carbonate leaching were observed. In conclusion, the dynamics of the carbon system in this wetland are modulated by hydrological seasonality, local geology, and biological activity, which determine high variability and limited buffering capacity against acidification. These findings highlight the importance of including karst wetlands in environmental monitoring and management programs under climate change scenarios.