The bulk of Historical Manuscripts and Notes includes Onderdonk's transcriptions, abstracts, and notes from various church and local government records, private journals, and newspapers. The series includes a small number of print versions of Onderdonk's works and of manuscripts of Onderdonk's own writing. Most of the documents in the series concern towns in nineteenth-century Queens County (which included present-day Nassau County), but towns in Suffolk County are also represented. The series also holds material on towns in Kings County, though to a lesser extent than other Long Island locales.

Many of the documents in the series have a topical focus, with the principal subjects concerning the American Revolution, Quakers (or Friends), and agriculture, including animal husbandry. These documents include transcriptions of Revolutionary-era correspondence to Major John Kissam of the Queens militia and of Quaker John Bowne's journal of imprisonment and account book. Documents concerning "olden times" are more wide-ranging, spanning social issues, commercial ventures, agriculture/farming, crime, church/religion, politics/governance, slavery, etc. Many documents are principally lists of marriages, deaths, baptisms, wills filed with the surrogate's office, tax lists, etc. Some of the manuscripts include an index.

Many of the notebooks in the series were constructed from previously-used documents, especially correspondence from circa 1870s to the clerk of Queens County, but also advertisements and other printed matter. Onderdonk wrote on the blank reverse sides of these documents, and much of the original content can still be viewed. A substantive example is an account book of fees received in 1866-67 by surrogate William H. Onderdonk.

Aside from the original artifacts comprising many of the notebooks themselves, there are few original records in the series. Significant exceptions to this are the wampum, bills of credit and paper currency attached to pages of Onderdonk's historical sketch of agriculture. Some of the notebooks include paper slips with signatures; it is not clear whether these are original signatures cut from documents or Onderdonk's tracings of the original signatures.

The Correspondence series includes the extensive correspondence sent to Onderdonk by historians, genealogists, librarians, and others. This correspondence both requested information of Onderdonk and provided information at his request. The mutual support between Onderdonk and his correspondents in their historical research endeavors is apparent throughout the series.

As described in the Arrangement Note, the series has four sets of correspondence. These sets are more a reflection of Onderdonk's filing systems, Brooklyn Historical Society's past processing practices, and the varied sources of the correspondence than of any substantial difference in content or chronology. Accordingly, the general themes of the correspondence are consistent across the sets, and many of the correspondents are found in more than one set. Nonetheless, each set has its own strengths:

A principal theme of Set 2-1 is the Revolutionary War, especially the Battle of Long Island and, to a lesser extent, the execution of Nathan Hale. The set also includes notes on genealogy, acknowledgements of receipts of Onderdonk's published works by individuals, libraries, etc.; invitations to readings, college commencements, celebrations, meetings, etc.; and requests of Onderdonk for historical and family history. Much of the correspondence takes the form of responses to specific Onderdonk requests for information, publications, etc. The bound correspondence includes some transcriptions of Long Island town records, including those of Jamaica, Flushing, and Hempstead. Hempstead history is a notable subject of the bound correspondence. Substantive correspondence in the set comes from authors and historians James Fenimore Cooper, George Bancroft, Charles Hoadly, Jared Sparks, Lorenzo Sabine, Thomas A. Strong, Benjamin F. Thompson, I.W. Stuart, and E.B. O'Callaghan. Other notable correspondents, though not necessarily conveying substantive matter, include John Breckinridge, James Buchanan, Washington Irving, William H. Seward, and Hamilton Fish, along with other U.S. senators, Congressmen, and state politicians. Correspondents that appear in other BHS collections include Henry Stiles, Henry Pierrepont, Jeremiah Johnson, and Henry Murphy.

Set 2-2 also principally involves genealogy, requests for information, sharing information about the availability of particular books, and the like. The set includes a folder of correspondence with or about Quakers (Friends). Most notable in this regard is a letter from Rachel Hicks discussing Elias Hicks and Gideon Seaman, along with Quakers on Long Island in relation to American Indians, slavery, and the American Revolution. Also included in this set is correspondence from Onderdonk's former classmates at Harvard College and other Boston-area correspondents. Notable correspondents in this set include Lyman Draper commenting on the State Historical Society of Wisconsin, historian Jeptha Root Simms and Columbia College librarian William Alfred Jones commenting on various historical works or events, and Long Island genealogist Benjamin D. Hicks. Onderdonk's indexes and lists of names for this set are found in each folder.

Set 2-3 includes requests of Onderdonk for information, publications, etc., and responses to Onderdonk's requests for same. The principal subject matter concerns genealogy, church history (especially Quakers and the Episcopal Church), and the American Revolution. Major correspondents include historians and genealogists Teunis Bergen, Jacob T. Bowne, Rev. Edward T. Corwin of Millstone, NJ, John J. Latting, and E.B. O'Callaghan. Other correspondents that can be found in BHS collections include Henry C. Murphy, Henry Stiles, and William S. Pelletreau. Requests for publications included correspondence from US senators and Congressmen, such as Roscoe Conkling, Hamilton Fish, and Dwight Townsend. A letter from William Pelletreau in the set's "miscellaneous research requests" referring to four beads of wampum may provide insight to the source of the wampum found in the Historical Manuscripts and Notes series. An 1875 letter from William Potts of Camden, NJ, surveys Quaker objections to slavery in New Jersey and Pennsylvania.

Set 2-4 includes an 1856 letter from future president James Buchanan acknowledging his induction to the Long Island Bible Society, James Fenimore Cooper writing of British general Oliver de Lancey, E.F. Ellet corresponding with Onderdonk concerning her histories of the American Revolution (which emphasized women and domestic matters), and Gideon Frost, John Hicks, Benson Lossing, and James Riker on sources and writings concerning Long Island Quakers and Revolutionary War history.

The series includes a variety of original historical documents such as handbills, petitions, fliers, programs, and financial records related to various Long Island communities. Queens County is especially well-represented in the series, including various original invoices for expenses related to the transportation, maintenance, and execution of prisoners in Queens County; electoral campaign materials for temperance candidate Simon Craft (1846), advertisements for James M. Huntting's English and Classical Family School (1857), a share of stock in the Jamaica Circulating Library (1861), and other matter. Documents related to Union Hall Academy of Jamaica include student petitions, a list of students (1847), an advertisement with tuition rates, rules and other information, and student exhibition programs. For present-day Nassau County, documents include the program for the laying of the cornerstone at the Cathedral of the Incarnation in Garden City (1877), a Hempstead Seminary advertisement (1837), notices for public celebratory events at Little Neck (1857) and Manhasset (1872), and a 1793 document dividing land (likely at Cow Neck) between James Hewlett and George Rapelje. The series includes genealogical research notes and correspondence for the Dodge family of Long Island, a transcription of a French and Indian War era (1758) muster roll and related notes concerning a New York battalion from a regiment commanded by Col. Oliver de Lancey, and an account from a doctor's daybook showing services rendered (1729-1731).

The series includes eight scrapbooks compiled by Onderdonk in the 1860s. Seven of these scrapbooks, completed in 1869, comprise a set covering Queens County, which at the time also included the towns that would later become Nassau County. In these volumes, Jamaica, Flushing, and Hempstead are perhaps most prominent, but other locales, including Newtown, Oyster Bay, Cow Neck, Roslyn, and Glen Cove, are represented significantly. Occasional Kings County material appears, though not extensively; generally this material especially concerns Brooklyn and are often clippings from a series of historical pieces published by the Eagle. The bulk of the material consists of newspaper clippings; it is seldom clear which newspapers were the source of particular clippings, but at least three newspapers appear to have been significant sources: Democrat (Jamaica); Long Island Star; and Long Island Farmer and Queens County Advertiser. Some handbills, advertisements, circulars, and other such ephemera can also be found in the scrapbooks; in most instances, these items date from after the scrapbooks compilation date and are tipped-in at seemingly random places, such as a circa 1880 Manhattan Beach Railway timetable and map found in Volume 2.

The clippings focus on Queens County matters of potential local historical interest, so broader New York or national events are not represented aside from their local connection, nor are literary or other fictional writings included. The subject matter of the clippings is wide-ranging, but there is also a high level of consistency across the seven volumes for several subjects. These subjects include political matters, such as accounts of political gatherings, detailed results by town of presidential, state, and local elections, and party positions; agriculture, such as agricultural society fairs (especially the Queens County Agricultural Society) and lists of premiums awarded by the societies; temperance and temperance societies; government matters, such as accounts of town meetings, meetings of town trustees or supervisors, and court proceedings; announcements, public notices and advertisements, such as those for public auctions, lectures to be given, openings and other events at schools, churches, and other institutions, camp meetings, stagecoach departure schedules, and recreational outings and events; financial information, such as taxpayer lists and assessments, town finances, and corporate operations; crimes (e.g., murder, rape, assault, theft) and accidental deaths (e.g., drownings, fires, falls); lists of interments; July 4 celebrations, including accounts of the toasts given; and railroad development and reports of operations. References to African-Americans, though not frequent, appear throughout the volumes in the context of the above subjects, such as runaway notices (Vol. 1), announcements of camp meetings (e.g., Vol. 4) or annual beach parties (Vol. 6 and 7), and in accounts of crimes, accidents or deaths.

The first volume includes Revolutionary War events, including information on the prison ships and the refugees from Long Island. Volumes 6 and 7 include much on the Civil War as it relates to Queens County, such as town war meetings, lists of draftees, deaths, and regiment recruitment, musters, and other activities. Items with an obvious personal connection to Onderdonk are common, including material on Union Hall Academy and articles referring to individuals with the Onderdonk name. By 1866, the scrapbooks include box scores and summaries of local baseball games. The eighth scrapbook in the series was compiled at an earlier date, in 1864, than the seven volume set. The single volume includes Kings and Suffolk counties in its scope, as well as Queens County. The subject matter of this one volume is generally consistent with that described above. Because of the overlap in chronology, the Queens County section of this scrapbook can be viewed as a supplement to the seven volume set. The Kings County section of this scrapbook consists principally of a series of historical narratives published by the Brooklyn Eagle circa 1862.