The Amazonian manatee (Trichechus inunguis) is endangered due to illegal hunting. In Peru, the Centro de Rescate Amazónico (CREA) rehabilitates and releases rescued manatees. Tree females and two males were released in El Dorado Lake in July 2011 and radio tracked until November 2011. Movements, habitat use and behavior recorded during the post-release period were used to evaluate the manatees’ adaptation to free-living conditions. A total of 140 locations was registered during 91 days of tracking. Females showed greater residence time than males, which migrated out of the lake. Females selectively used the micro habitats of the study area, preferring floating vegetation, followed by open water and lastly shore macrophytes. Most idling behaviors were registered in areas with floating macrophytes, and open water was mainly used for traveling. No correlation between sighting hour and sighting location (micro habitat type) was detected. The use of suitable zones, in addition to natural behavior, suggests that these rescued manatees responded well to free-living conditions after release. Some considerations are provided with the purpose of strengthening manatee rehabilitation programs and improving future releases, emphasizing the importance of choosing appropriate individuals, as well as suitable areas and times to help improve release outcome.