Ninety-four percent of the land of Megantoni is protected for conservation or allocated to indigenous people. The majority of this land is almost untouched tropical rainforest and Peruvian Yungas characteristic of the Amazon Basin and the eastern flanks of the Andes. Protected lands include the Pongo de Mainique, a scenic water gap where the Urubamba River cuts through the Vilcabamba mountain range on the southern border of Megantoni. East of the Pongo, the Megantoni National Sanctuary straddles the border with Echarate. The Kugapakari-Nahua-Nanti Indigenous Territorial Reserve covers most of the eastern one-half of the district. The Otishi National Park and the Machiguenga Communal Reserve straddle the western border of the district. Both the reserves were created to protect the lands and the voluntary isolation of some groups of indigenous people.