Series II. William Ingersoll Bowditch Papers consists of family letters, business papers, and material from his studies at Harvard during the 1830s. Manuscripts, copies of many of Bowditch's speeches and pamphlets, and numerous clippings on anti-slavery and women's suffrage are also included. This series has been subdivided into four subseries.

Subseries A. Correspondence contains correspondence with family and friends, which is arranged alphabetically by correspondent name.

Subseries B. Others' Correspondence contains letters between reformers including that of William Lloyd Garrison, Francis Jackson, Lydia Maria Child, Theodore Parker, Susan B. Anthony, and Samuel May.

Subseries C. Financial and Legal Papers contains receipts, accounts, bills, legal documents, and obituaries as well as a plot plan of his lot in Brookline.

Subseries D. Writings includes original manuscript versions of books, printed pamphlets, and articles as well as a journal and school notebooks. This subseries has been organized into four sub-subseries. Sub-subseries 1. Personal (Academic) contains Bowditch's handwritten notebooks from his academic work at Harvard College and Harvard Law School as well as an article that he wrote for the Boston Globe about his college class of 1838. Sub-subseries 2. Genealogical (Family History) contains background material on Bowditch family members, handwritten manuscript drafts, and the final version of Our Family Story from 1639 to 1838, which was published in 1896. Family Letters, etc. collected by William I. Bowditch, 1906 contains original letters, maps, music, and photographs of Nathaniel Bowditch, Nathaniel Ingersoll Bowditch, Jonathan Ingersoll Bowditch, Charles Ingersoll Bowditch, Henry Ingersoll Bowditch, Mary Ingersoll Bowditch, wife of Epes S. Dixwell, and Elizabeth Boardman Ingersoll Bowditch, wife of John James Dixwell. William I. Bowditch's Life Volume II, 1907 details his activities on anti-slavery, women's suffrage, aiding discharged convicts, and the Plummer School [Salem, Massachusetts]. Sub-subseries 3. Anti-slavery contains notes and original manuscripts of various publications that Bowditch published in the late 1840s and 1850s. Reply to Mr. Peabody was a series of newspaper articles. Sub-subseries 4. Women's rights contains notes, manuscripts, and printed articles that Bowditch wrote in the 1870s and 1880s.

Subseries E. Clippings and Printed Material contains newspaper clippings and pamphlets on subjects in which Bowditch was interested, mainly slavery and women's suffrage.