This study evaluated the physicochemical characteristics, organic matter content, and heavy metal accumulation in the sediments of four Andean lakes in central Ecuador, considering their trophic states and protection status. A total of 96 sediment samples were collected and analyzed for electrical conductivity, pH, organic carbon, phosphorus, and heavy metal concentrations (Fe, Mn, Ni, Zn, Cu, Pb). The ecological risk was assessed using the potential ecological risk index (PERI) and pollution load index (PLI), and significant environmental predictors were identified using a classification and regression tree (CART) model. The results showed that protected lakes (Atillo and Magdalena) exhibited higher concentrations of Fe, Mn, and Ni, predominantly from natural sources, while unprotected lakes (Colta and Yambo) had greater Pb and Cu enrichment, associated with anthropogenic inputs. The PERI and PLI indices confirmed a low ecological risk across all lakes, although localized contamination was detected in Yambo and Magdalena. The CART model identified pH and phosphorus as the most significant predictors in protected lakes, whereas heavy metals and phosphate were more influential in unprotected lakes. These findings underscore the role of conservation status in shaping sediment composition and emphasize the need for targeted management strategies to mitigate anthropogenic impacts on Andean aquatic ecosystems.