In 1870 Henshaw traveled to Florida with naturalist Charles Johnson Maynard and artist Edwin Lord Weeks.

In 1872 Henshaw went to Salt Lake City on the Wheeler Survey as a naturalist, and in 1874 had his most successful field expedition, going from Santa Fe, New Mexico to Gila River and south-western Arizona.

[2] Along with C. Hart Merriam and Grove Karl Gilbert, Henshaw set out West on the United States Geological Survey, where in addition to his ornithological work, Henshaw worked on linguistics and anthropology, eventually compiling two volume book titled Handbook of North American Indians North of Mexico.

The result of that publication was the National Geographic Field Guide to Birds of North America.

While not working with the National Geographic, Henshaw lobbied, along with George Shiras, to pass the Weeks-McLean Act, otherwise known as the Migratory Bird Law.

Henshaw was one of the founders of the Nuttall Ornithological Club in 1873, the American Ornithologists' Union in 1883, and the National Geographic Society in 1888.