Fish belonging to several trophic levels from Cartagena Bay, a tropical estuary, were collected and analyzed for total mercury (T-Hg) concentrations in muscle. T-Hg concentrations varied from 0.010–0.526 μg/g, and the overall average was 0.051 ± 0.002 μg/g. Carnivorous species presented the highest T-Hg mean value (0.100 ± 0.006 μg/g), followed by omnivorous (0.076 ± 0.014 μg/g) and detritivorous (0.028 ± 0.001 μg/g). The relationships between weight and T-Hg content were found for the carnivorous species Sciades herzbergi (r = 0.508, p < 0.001) and not for the detritivorous Mugil incilis (r = 0.086, p = 0.207). Although results suggest fish from the bay pose a low health threat for humans in terms of Hg exposure, vulnerable groups such as pregnant women, should avoid eating large size carnivorous species. Knowledge about species with low Hg content should be widespread within fishing communities, guaranteeing adequate nutrition by including fish in the diet and reducing the risk of Hg poisoning.