We investigated the seasonal carbonate chemistry variability within a semi-enclosed tropical mangrove lagoon in southwestern Puerto Rico. Biweekly measurements of seawater temperature, salinity, total alkalinity (TA), and dissolved inorganic carbon (DIC) were conducted from 2014 to 2018. We describe the possible mechanisms driving the observed variability by correlating the DIC/TA ratio with pH and Ωarg, suggesting that the mean pH (7.87 ± 0.09) and aragonite saturation state (Ωarg, 2.96 ± 0.47) of the mangrove lagoon negatively affected calcification. The measured pCO2 and DIC/TA ratios indicate that heterotrophic activity was the primary driver for persistent acidification, which reached its maximum expression during the wet season. We conclude that mangrove lagoons with limited seawater exchange and high carbon input will not mitigate ocean acidification.