Puerto Maldonado is located in the lowland Amazon rainforest, only 55 km from the Bolivian and Brasilian borders; on the confluence of the Tambopata and Madre de Dios Rivers. The climate is tropical. The chief industries in Puerto Maldonado are logging, gold dredging, brazilian nut collecting, boat building and eco-tourism. A ferry crosses the river, linking the main road from Cuzco.

Nearby are the Manu and Tambopata-Candamo national parks and the Bahuaja-Sonene national reserved area. These are some of the most pristine primary rain forests in the world.

Puerto Maldonado counts with a good airport, with daily regular flights to Cusco and Lima.