Series I consists of 42 diaries belonging to Paine, and one diary belonging to his wife, Catherine J. Paine.

Paine's diaries document both his professional and private life. His early diaries (1848-1860) document his travel from New Hampsire to Sheboygan, Wisconsin and from Wisconsin to California during the Gold Rush. His diaries documenting his experiences while traveling to and in California during the Gold Rush are particularly detailed. In these entries, Paine records his observances of several mining regions in California paying particular attention to sites in El Dorado, California including Placerville, Sutter's Creek and Spanish Flat. Paine documents the towns specifically as well as mining engineering and prospecting in general. Paine also documents his travel back to Sheboygan by boat with stops in Mexico, Panama, San Juan, the West Indies, Havana and New York City; completing the route by railroad through Michigan and Illinois.

Paine's 1860-1865 diaries detail his work as a topographical engineer for the Army of the Potomac. These entries are largely written during his time in Washington D.C. and Virginia. Additionally, Paine has diaries from this time period that consist of departmental orders, headquarter notes and accounts related to his military work.

Paine's later diaries (1865-1890) are largely written while he was living in Brooklyn, N.Y. and consist mostly of personal entires. There are only two diaries from Paine's time working on the Brookyln Bridge, with little mention of his specific work. Throughout his diaries, Paine talks frequently of religion, often citing sermons he attended.

The diary of Catherine J. Paine has very few entries, and appears to be largely written after William Paine's death in 1890.

Series II consists of personal correspondence both written and received by Paine and includes letters from military headquarters and correspondence with family members and colleagues. The correspondence includes information regarding Paine's work as a surveyor for the Union Army, the transfer and management of family property,family relationships, and engineering and military pensions. Included is correspondence addressed to Paine's widow, Catherine Jone Paine regarding settlement of his affairs after his death in 1890.

Series III consists of letters of patent held by Paine, reports of examination and promotional material. The letters of patent are offical documents issued by the government including the specification and illustrations of the patented item. The reports of examination are reports on the patentability of a product or item, conducted in response to a patent application. The promotional material is in regards to Paine's Patented Steel Measuring Tapes and includes specifications and pricing.

Series IV consists of architectural and engineering documents related to Paine's work as a civil engineer. The Hudson River Tunnel specifications consist of reports related to Paine's consulting work evaluating the progress of tunnel construction and specifications of pneumatic tunneling equipment. Included in these records is a note regarding potential safety issues encountered during tunnel construction.

The engineering notes include information regarding various civil engineering projects, topics and equipment focusing on rapid transit, suspension bridges and cable railways. It also includes calculations and one drawing of a pneumatic tunneling apparatus.

Series V consists of engineering reports, journals, one bible, maps, and the program of the opening ceremonies of the Brooklyn Bridge. The three engineering reports consist of one report on the Niagra Railway Suspension Bridge and two on the East River (Brooklyn) Bridge. Journals consist of one issue of a circa 1869 weekly periodical, "The Volunteer". The maps in this series consist of five maps; three military maps of Virginia published by the War Deparment, one map of Philadelphia and Camden and one map of gold regions in California. Paricularly of interest is the 1852 "Gold Regions in California" map. The map is in full color and includes technical annotations by Paine.

Series VI consists of financial records including receipts, records of patent taxes, and stock certificates.

Series VII consists of personal legal documents including contracts and documents related to real estate and family property. Also included are documents related to the settlement of Paine's affairs after his death in 1890, handled by his widow Catherine J. Paine. These documents contain information about personal affairs as well as settlement of Paine's business affairs and sale of patents.

Series VIII consists of clippings and notes related to Paine's work and interests as a civil engineer, both independently and for the Union Army. Included are clippings about Paine's civil engineering projects as well as other general projects and technologies.

The notes consist of general notes likely taken by Paine on various subjects including his work and religion. Also included are notes documenting the genealogy of the Paine family.

Series IX consists of ephemera largely related to Paine's work as a civil engineer. The general ephemera consists of programs, tickets, business cards, stationery and various other materials. This includes a small book of photographs of the East River (Brooklyn) Bridge. Also of note is an 1865 anti-slavery poster - a graphic representation of politicians who supported the abolition of slavery. General ephemera also includes promotional material, maps and programs from the 1893 World's Fair, belonging to Paine's daughter Kathreen. The memorial and commemorative ephemera consists of memorial service programs, obituaries, and other articles in commemoration of Paine's work, written after his death.

Two locks of hair are also included in ephemera, one belonging to Colonel Dalgren, and one unlabled.

Commisions and certificates consists of four Civil War commissions, one certificate honoring Paine from the American Society of Civil Engineers and one certificate from the Packer Collegiate Institute regarding the education of Kathreen Paine. Two of the Civil War commissions are signed by Abraham Lincoln and two by Andrew Johnson.

Series X consists of photographs of the Paine family, as well as Civil War era military photographs. One album of Civil War military portraits included several photographs attributed to notable Civil War photographer Mathew B. Brady. Also included in this series are three albums of undated Paine family photographs as well as loose photographs. Additionally, there are six albums of photographs that belonged to Paine's daughter Kathreen Paine, dating from 1915 to the mid 1930s.