Crocodylus moreletii (Morelet’s crocodile) and Crocodylus acutus (American crocodile) are generalist, apex predators of subtropical aquatic habitats in Central America. As top predators, crocodiles may be exposed to high levels of micro pollutants, such as trace elements via bioaccumulation that enter the food web as a consequence of human activities. As such, the status of their population can be considered indicative of that of the entire ecosystem – i.e., crocodiles constitute as genuine indicator species. In this study, we report on the concentrations of trace elements found in the caudal scutes of 178 specimens of C. acutus and C. moreletii from Belize. Our objectives were three-fold: (1) to assess variation in trace element concentration between species, sexes, age classes and body index; (2) to identify areas with elevated exposure to trace elements by comparing concentrations in the scutes of crocodiles at various sites in Belize; and (3) to explore links between crocodile trace element load and local land use. All elements tested (Hg, Pb, Cd, As, Cu, Zn, Co) could be detected in at least some scutes. Many of the readings of As and Co were under or close to the detection limit and were not further analyzed. Relatively high Hg concentrations were observed in adults from Chiquibul Forest (median 3.170 µg/g) and Ambergris Caye (0.834 µg/g). Concentrations of Hg and Pb tended to be higher in adult animals than in juveniles, especially in C. acutus. On the other hand, concentrations of Cd, Cu and Zn were higher in juveniles than in subadult adult animals. Concentrations of Cu were higher in C. acutus than in C. moreletii, but otherwise no species-effects were found for the other trace elements. We found a negative correlation between Hg and Zn concentrations; correlations among Cd, Pb, Cu and Zn concentrations tended to be positive. In both juveniles and adults, animals with high concentrations of Zn had lower body-indices (a proxy for physiological condition). None of the other element concentrations correlated with the body-index. Specimens of C. acutus were more often sampled at coastal sites, while C. moreletii sampling points were typically closer to agricultural or forested areas. A canonical correlation analysis revealed a significant association between trace element load and habitat characteristics. Animals sampled inland, near submontane forests, contained higher levels of Hg, while animals sampled near agricultural, urban or lowland habitats tended to have higher concentrations of Cd, Pb, Cu and Zn. This study identifies the most prevalent trace element concentrations impacting Belizean watersheds while highlighting the exposure risk to non-essential trace elements in less-urbanised areas or protected areas.