Coastal ecosystems face increasing anthropogenic pressure, driving acidification and shifting them from carbon sinks to sources, yet comparative assessments across contrasting catchment types remain limited, particularly in the Indian Ocean region. We investigated carbonate chemistry in two contrasting tropical Sri Lankan lagoons, Negombo Lagoon, impacted by intensive anthropogenic and marsh-derived inputs, and minimally disturbed Rekawa Lagoon. In Negombo, low-pH, low total alkalinity (TA), and high-CO₂ river water and acid-sulfate marsh inputs, combined with weaker carbonate buffering, intensified acidification (pH = 7.66 ± 0.45) and sustained CO₂ outgassing (9.1 ± 10.2 mmol m^-2 d^-1). The lowest pH and weakest buffering occurred in the inner lagoon, and increased toward the seawater inlet through river-sea mixing. In contrast, catchment-derived higher-pH, higher-TA, lower-CO₂ river water and strong buffering in Rekawa supported higher pH (8.31 ± 0.52) and net CO₂ uptake (−1.8 ± 0.9 mmol m^-2 d^-1). Our simulations showed that riverine alkalinity enhancement (292–526 µmol kg^-1 TA addition) mitigated acidification and CO₂ outgassing in Negombo within 40–50 days. Our regional data synthesis showed that pH increased significantly with increasing TA/DIC ratio across estuaries and lagoons. These findings highlight carbonate buffering and catchment management as key strategies for mitigating coastal acidification and CO₂ emissions.