Wetlands are critical ecosystems globally, boasting significant ecological and economic value. They play a crucial role in the hydrological cycle by storing water and carbon, thereby helping to mitigate climate variability. But in Panama, little is known about the carbon stored in freshwater wetlands. This research presents the estimation of the carbon stocks of two freshwater wetlands in Panama, located on both sides of the Caribbean (Portobelo) and Pacific (Tonosi) coasts. The methodology consisted of transects of 125 m and 40 m wide, with six circular plots every 25 m; in each transect, the diameter of the tree trunk was measured at breast height (1.3 m) and the species was recorded, and in the same plots, soil samples were collected in triplicate by depth intervals. The average total ecosystem carbon storage (TECS) for the aquatic wetlands of Tonosí was 106.26 ± 18.3 Mg C ha−1, and for Portobelo, it was 355.09 ± 70.02 Mg C ha−1. These recorded values can contribute to the conservation of wetlands, supporting Panama’s nationally determined NDC contributions. However, despite the acceptance that wetlands are important nature-based solutions, national data on soil carbon stocks in freshwater wetlands are still scarce and their protection should be increased.