The Margaret Atherton Bonney papers date from 1810 to 1992 and measure 12.25 linear inches. The papers consist of Bonney's research materials and are arranged in 4 series: Mary Jane Coggeshall, Abner Kneeland, Jennie McCowen and Mary Louise Duncan Putnam.

The Mary Jane Coggeshall series consists of the biographical material Bonney collected while preparing Coggeshall's nomination to the Iowa Women's Hall of Fame, to which Coggeshall was inducted in 1990. Materials include a detailed biographical sketch and supporting documents. Also included in the series is correspondence regarding the research and nomination process, a copy of the acceptance speech given by Bonney at the ceremony, and a photograph of Coggeshall.

The Abner Kneeland series is the largest in the Bonney papers and consists of several sub-series: Biographical research materials, Contextual research materials, Correspondence, Grace Boler Forgrave, Research notes, Secondary Sources and Books. For the most part, the titles of individual folders match the original titles used by Bonney. The Biographical research materials consist of photocopies of Kneeland's daybook and his letters to the Boston Investigator in 1839 and 1840, genealogical material, newspaper clippings and a 1903 speech regarding Kneeland. There is also a photograph of the Kneeland home built in Salubria in 1840. The Contextual research materials consist of photocopies and notes regarding city directories, censuses, county records and maps. The Correspondence is between Bonney and those interested in her research. Grace Boler Forgrave was Kneeland's granddaughter and this sub-series contains a memoir in which she wrote about her grandfather and a handmade booklet of some of Kneeland's original hymns. The Research notes include biographical information and Bonney's handwritten records of the libraries and archives she visited and what they contained. There is also an interesting collection of Bonney's thoughts regarding John Cleland, the author of the 'infamous' book Fannie Hill, speculating on whether or not he and Kneeland were related. The Secondary sources sub-series consists of both original and photocopied articles regarding Kneeland spanning the years 1868 through 1950. The Book sub-series consists of original texts owned or written by Kneeland. These include his 1827 Key to the New System of Orthography, his 1836 National Hymns: Original and Selected and his 1823 translation of The New Testament.

The Jennie McCowen series consists of the materials Bonney collected while preparing her nomination of McCowen for the Iowa Women's Hall of Fame, including biographical information, articles by and about McCowen, newspaper articles, and Bonney's correspondence.

The Mary Louise Duncan Putnam series consists of the materials Bonney collected while preparing her nomination of Putnam for the Iowa Women's Hall of Fame. The series includes a detailed sketch of Putnam's life and achievements, articles about The Davenport Academy of Science, newspaper articles, obituaries and memorial tributes for Putnam, and Bonney's correspondence.