Established by Manuel Pacaya–Samiria, a leader of the Cocama peoples, following the 1830 uprising at the Jesuit mission of Lagunas, Nauta soon became the primary commercial hub of the Peruvian selva baja. In 1853, a Brazilian owned paddle steamer made it all the way to Nauta.
Nauta is the primary destination of the only major road leading out of Iquitos, and is a staging area for several ecotourism lodges and ships on the Marañòn River. Boats take passengers from Nauta to the Pacaya-Samiria National Reserve.
In 2013, residents of Nauta created a children's rap video in the Kukama-Kukamiria dialect, in collaboration with Radio Ucamara. The local radio station has been involved in conserving the language for "a few years," and "started managing a school called Ikuar, with the goal of teaching the language through songs and traditional story telling."