He worked for over 51 years in the Ornithology Department at the Academy of Natural Sciences of Philadelphia, and served in multiple roles including as Director from 1925 to 1928.

He published several books and hundreds of articles on birds, flora, and mammals with a focus on Eastern Pennsylvania and South Jersey.

The Witmer Stone Wildlife Sanctuary in Cape May Point, New Jersey, was established in 1935 by the National Audubon Society and named in his honor.

[4] In March 1888, he was appointed a Jessup Fund Student at the Academy of Natural Sciences of Philadelphia, and helped organize their extensive collection of birds.

[8] Stone participated in hundreds of academy sponsored field expeditions to the Pine Barrens and coastal regions of New Jersey.

He also participated in field expeditions to various locations including Arizona, Bermuda, Kentucky, Maryland, Mexico, Minnesota, and South Carolina.

[10] His focus was ornithology, but Stone also had a good knowledge of crustaceans, insects, mollusks, reptiles and the local flora.

[11] The Dutch botanist Frans Stafleu stated that "Stone's concentration on ornithology was a definite loss for botany.

It has been described as “the only comprehensive floristic treatment for southern New Jersey and it continues to be used today [2002].”[10] Stone's first ornithology manuscript was “The Turkey Buzzard Breeding in Pennsylvania” published in American Naturalist in 1885.

He founded the DVOC publication Cassinia and published multiple scientific papers, club activities and memorials.

[13] Stone was elected an Associate of the American Ornithologists’ Union (AOU) in 1885; a Fellow in 1892; and a member of the council in 1898.

The bulk of the work consists of species accounts of all the birds that had been found in Cape May County at the time of the writing, with their historical occurrence in the state and notes on seasonality, habits, and behavior gleaned from Stone's notes and the records of fellow DVOC members.