Bahía Salado, located in northern Chile (27°41’S, 70°59’W), is the southernmost foraging ground for the endangered green turtle (Chelonia mydas) in the Eastern Pacific Ocean (EPO). To date, almost no information exists on its current status, nor on its connectivity with nesting rookeries in the EPO. This study aims to inform on the genetic characterization, health and ecology of Bahía Salado’s green turtle aggregation in order to provide baseline information for local conservation strategies. We describe population structure and residency times using mark-recapture method. We also examine health parameters (body condition index, blood profile and blood copper-Cu and lead-Pb concentrations) and regional connectivity through genetic analyses. Our results indicate that this aggregation is composed exclusively of juveniles, with residency times varying between five to sixteen months. Turtles exhibited a very good body condition; however they showed the highest blood concentrations of Cu and Pb described for C. mydas and for almost all sea turtle species. Some biochemistry parameters (albumin, calcium, phosphorus, AST, triglycerides and creatinine) are also the highest ever reported for this species in the region. Analysis of the 770 bp (base pairs) control region of the mitochondrial DNA revealed four haplotypes, suggesting a strong genetic connectivity to the Galapagos rookery. Our study indicates that Bahía Salado’s aggregation represents a developmental foraging ground, where juvenile green turtles thrive. Although Bahía Salado’s ecosystem seems to be a very suitable habitat for the species, the high levels of Cu and Pb, together with elevated AST, demand further research on the negative impacts of heavy metals on this aggregation. Our results highlight the importance to protect this bay from anthropological activities, evaluate pollution sources and other local threats to this particular coastal ecosystem. We recommend year-round monitoring of the green turtle aggregation and other components of this ecosystem, incorporating participation of local seaweed collectors and the fishing community.Bahía Salado, located in northern Chile (27°41’S, 70°59’W), is the southernmost foraging ground for the endangered green turtle (Chelonia mydas) in the Eastern Pacific Ocean (EPO). To date, almost no information exists on its current status, nor on its connectivity with nesting rookeries in the EPO. This study aims to inform on the genetic characterization, health and ecology of Bahía Salado’s green turtle aggregation in order to provide baseline information for local conservation strategies. We describe population structure and residency times using mark-recapture method. We also examine health parameters (body condition index, blood profile and blood copper-Cu and lead-Pb concentrations) and regional connectivity through genetic analyses. Our results indicate that this aggregation is composed exclusively of juveniles, with residency times varying between five to sixteen months. Turtles exhibited a very good body condition; however they showed the highest blood concentrations of Cu and Pb described for C. mydas and for almost all sea turtle species. Some biochemistry parameters (albumin, calcium, phosphorus, AST, triglycerides and creatinine) are also the highest ever reported for this species in the region. Analysis of the 770 bp (base pairs) control region of the mitochondrial DNA revealed four haplotypes, suggesting a strong genetic connectivity to the Galapagos rookery. Our study indicates that Bahía Salado’s aggregation represents a developmental foraging ground, where juvenile green turtles thrive. Although Bahía Salado’s ecosystem seems to be a very suitable habitat for the species, the high levels of Cu and Pb, together with elevated AST, demand further research on the negative impacts of heavy metals on this aggregation. Our results highlight the importance to protect this bay from anthropological activities, evaluate pollution sources and other local threats to this particular coastal ecosystem. We recommend year-round monitoring of the green turtle aggregation and other components of this ecosystem, incorporating participation of local seaweed collectors and the fishing community.