The Arthur H. Clark papers contain a combination of personal papers, papers relating to Clark's time as a ship master and captain, both on private yachts and steamships involved in the China trade, materials from his maritime research, and some scrapbooks. This collection has been divided into five series.

Series I. Personal Papers contains photographs of Clark, legal papers, and personal correspondence. The legal papers include an award against Clark, in favor of James Gordon Bennett, and Clark's will along with two codicils. There are bills and receipts for artwork, and invitations and passes given to Clark over the years, including material related to the launching of the armored cruiser U.S.S. New York in 1891. Included in this series is a note about a portrait of Clark when he was on the Indiana; it appears that the note was written by former Peabody Museum Curator Lawrence W. Jenkins, but there is no information about why the note was written or when. Also included are materials related to a photography exhibit by Clark at the St. Botolph Club, a street directory, and Clark's obituaries. There is also an auction catalog from Karl and Faber included in this series. It is dated 1931, nine years after Clark's death, so it is unclear who added this to the collection or why, but it has been placed in this series because some of the auction items fall under Clark's research interests.

Series II. Ship Master, Agent, and Underwriter Business Papers contains four subseries. Subseries A. Non-steamship Papers contains materials from Clark's work on various yachts and other vessels that were not steamships. This includes the yacht Alice, a broadside from the 1859 Boston Regatta, and the cutter Margery Dow. Subseries B. American Steamship Company contains papers related to Clark's time with the company. This includes items such as recognition of Clark's time with the company and his resignation from the company. This subseries also includes a collection of letters from passengers praising Clark as a captain. Subseries C. Suwo Nada contains material relating to the steamship Suwo Nada, which Clark commanded, until it struck a rock and subsequently sunk in 1869. The subseries includes a certificate of survey, clearance papers, protests, testimonies, and articles about the sinking.

Subseries D. Underwriter and Agent Papers contains materials from Clark's time as an underwriter for a number of marine insurance underwriters, including the Boston Board of Underwriters, as well as material from Clark's work as an agent for Lloyd's of London, in New York. Subseries E. Industry Related Papers contains professional certificates earned by Clark, and letters of recommendation. The subseries also includes industry related materials such as an employee manual from the Shanghai Steam Navigation Company, and news clippings about the financial problems of the Hong Kong Pier and the Godown Company.

Series III. Publications contains publications by Clark and reviews of those publications. This includes a series of letters-to-the-editor of the New York Evening Post, "Clipper Ships and their Records" by Clark, and publication announcements and reviews of Clark's History of Yachting.

Series IV. Research contains research related notes, articles, transcriptions of articles and excerpts from larger works, inquiries, and correspondence related to Clark's various research topics. This series contain four subseries. Subseries A. History of Yachting contains research materials related to the history of yachting from the 16th to the 19th centuries. This includes articles removed from journals, and transcriptions from larger works. Subseries B. Clipper Ships contains research materials related to the history of clipper ships. This includes correspondence regarding research requests made by Clark, articles removed from journals, newspapers, and magazines. Subseries C. Maritime Related Research contains research from various related topics such as lists of goods shipped, ship building, and prominent naval figures. Included in this subseries are journal articles, transcripts of larger works, and news clippings. Also included in this subseries is a folder of illustrations that have been removed from various publications; some of these were removed from Clark's scrapbooks. The material was separated with the comment "Newspaper cuts, etc., some to mount for [Marine Room] cab". Subseries D. Marine Society Research contains material related to Clark's proposed book From Galley to Galleon: The Ships and Sailors of Early Days. The book was going to be published posthumously by the Marine Research Society as publication number 23, but it never was. There is correspondence requesting previously published images, photographs and prints, an edited manuscript (separated into two folders because of its size), and advertising materials. It should be noted that the advertising materials are unrelated to Clark or his manuscript, but were filed in the same folder as his editor's correspondence with publishers, so they have been left together; it is unclear who added them to the collection or why—for example, there is a memorandum from the Massachusetts office of the state quartermaster advertising captured German war trophies available for sale to select organizations, dated 1927.

Series V. Scrapbooks contains three scrapbooks. The first scrapbook contains transcriptions of logbook entries, articles, abstracts of letters, news clippings, and correspondence to Clark. The second scrapbook is labeled "Letters Mounted and Not," it is unclear if this was Clark's title, and contains correspondence to Clark. The third scrapbook contains transcripts of articles, news clippings and journal articles. All of the scrapbooks relate to Clark's research on ships.