The Manuscripts and Employee Files series in this collection includes lectures given by Watkins, manuscripts written by Watkins, a collection of Southwest Society and Southwest Museum employee materials, and copies of Southwest Museum annual reports. These materials date from 1886-1963, but the bulk range from 1904-1953.

The Personal Papers series spans from 1912-1959 and includes correspondence, a scrapbook on personal achievements, and two scrapbooks on Tibet and the Dalai Lama, and papers documenting Watkins's student life. The student papers include manuscripts by Watkins from high school, manuscripts and correspondence from Watkins's years at University of Denver, a poetry file, and year books. This series also contains files relating to Watkins's pursuit of a PhD from University of Southern California, which include announcements, correspondence, and ephemera. Copies of Watkins's 1942 dissertation, The Crafts and Industries of the American Indian Women of California and the Southwest,are also included in this series.

The Subject Files series includes materials on both professional and personal interests, which are often intermingled, especially in the clippings files, and span from 1855-1968. This series includes a set of index cards containing bibliographies Watkins created on a variety of subjects, again reflecting both personal and professional pursuits. This series also includes Watkins's research files which may contain clippings, correspondence, images, maps, manuscripts, and notes. Watkins assembled a large collection of manuscripts by others, including extensive files on Charles Fletcher Lummis, George Wharton James, and Watkins's sister Margaret S. Watkins. The Lummis and James materials include correspondence, manuscripts, and clippings both by and about both men. Collected publications in the Subject Files series include brochures and pamphlets, with a large collection of travel literature from the 1930s-1950s. This series also includes collected images and artwork, including prints by E. A. Burbank.

The Publications series includes monographs and serials collected by Watkins, spanning from 1891-1961. Publications cover various topics similar to those in the Subject Files, including a large portion of travel brochures. Topics of publications include animals, art, botanical studies, California, celebrities, history, and natural history. Publications on travel refer mostly to California and Southwest destinations, but also include other sites in the United States, Europe, and other countries around the world.