Matthews was posted at Fort Union in what is now Montana in 1865. It was there that an enduring interest in Native American peoples and languages took root. He would go on to serve at a series of forts in Dakota Territory until 1872: Fort Berthold, Fort Stevenson, Fort Rice, and Fort Buford. He was a part of General Alfred H. Terry's expedition in Dakota Territory in 1867. While stationed at the Fort Berthold in the Dakota Territory, he learned to speak the Hidatsa language fluently, and wrote a series of works describing their culture and language: a description of Hidatsa-Mandan culture, including a grammar and vocabulary of the Hidatsa language and an ethnographic monograph of the Hidatsa. He also described, though less extensively, the related Mandan and Arikara peoples and languages. There is some evidence that Matthews married a Hidatsa woman during this time. Her name is not known. There is also speculation and circumstantial evidence that Matthews had a son with the woman. In April, 1876, Matthews was sent to Camp Independence to serve as Post Surgeon. In ensuing months he serviced soldiers and local civilians; he vaccinated hundreds of Native Americans of the Owens Valley against smallpox. During his stay in the Owens Valley he pursued other interests, such as collecting native plants. He sent his collection to Asa Gray, who named two of those new to science after him: Loeseliastrum matthewsii and Galium matthewsii. Camp Independence was closed in July, 1877. In 1877 he participated in an expedition against the Nez Perce, and again in 1878 against the Bannock. While serving at a prison on Alcatraz Island in San Francisco Bay, Matthews made a study of the Modoc language.
of the Smithsonian Institution'sBureau of American Ethnology suggested that Matthews be assigned to Fort Wingate, near what is now Gallup, New Mexico. It was there that Matthews came to know the people who would become the subject of his best known work, the Navajo. His work on the Navajo served to dispel then-current erroneous thinking about the complexity of Navajo culture: Matthews is said to have been initiated into various secret Navajo rituals. In his work he reported that the Navajo were ichthyphobic, having a taboo on eating fish. He theorized that "Living in a desert land where water is so scarce and so obviously important to life, water as sacred, it is an easy step for them to regard as sacred everything that belongs to the water…. Hence it becomes a sacrilege to kill the fish or eat its flesh."
