In order to enhance protection and conservation strategies for endangered green turtles (Chelonia mydas), the identification of neritic habitats where this species aggregates is mandatory. Herein, we present new information about the population parameters and residence time of two neritic aggregations from 2010 to 2013; one in an upwelling dominated site (Paracas ∼14°S) and the other in an ecotone zone from upwelling to warm equatorial conditions (El Ñuro ∼4°S) in the Southeast Pacific. We predicted proportionally more adult individuals would occur in the ecotone site; whereas in the site dominated by an upwelling juvenile individuals would predominate. At El Ñuro, the population was composed by (15.3%) of juveniles, (74.9%) sub-adults, and (9.8%) adults, with an adult sex ratio of 1.16 males per female. Times of residence in the area ranged between a minimum of 121 and a maximum of 1015 days (mean 331.1 days). At Paracas the population was composed by (72%) of juveniles and (28%) sub-adults, no adults were recorded, thus supporting the development habitat hypothesis stating that throughout the neritic distribution there are sites exclusively occupied by juveniles. Residence time ranged between a minimum of 65 days and a maximum of 680 days (mean 236.1). High growth rates and body condition index values were estimated suggesting healthy individuals at both study sites. The population traits recorded at both sites suggested that conditions found in Peruvian neritic waters may contribute to the recovery of South Pacific green turtles. However, both aggregations are still at jeopardy due to pollution, bycatch and illegal catch and thus require immediate enforcing of conservation measurements.