The William J. Beal papers consist of correspondence, publications, and materials relating to his work as a student at Harvard University. The material from Beal's years at Harvard includes course notes on anatomy, geology and ornithology as well as a detailed journal which Beal wrote in 1862. This journal includes comments on individuals as well as events of the period.

The correspondence is not extensive but contains several letters from Asa Gray as well as a typescript copy of a letter that Beal wrote in 1862 on the teachings of Louis Agassiz. The correspondence also contains a photocopy of an 1878 letter from Charles Darwin discussing hybrid corn. The volume listing Beal's publications is particularly useful since it gives a complete listing of all his writings from 1861 to 1921.