Disease, such as the Spanish flu epidemic of 1918, and workplace accidents occasionally felled inmates during their incarceration. Prisoners who died while incarcerated were not automatically buried in the Stoney Lonesome cemetery, only those whose relatives did not claim them. Fellow inmates attended funerals, which were overseen by local clergy or the prison's chaplain. Graves were dug by hand, usually by an inmate, and the coffins were pine boxes built in the prison's carpentry shop.
The cemetery is situated just north of the defunct prison complex along what is now an access road owned by the Fairfax Water Authority. It stands in a grove of cedar trees and is surrounded by a wrought-iron fence. Burials were laid out in north-south rows each containing 10-14 burials, and are discernible as depressions in the ground. A few rough grave markers are in place, but they do not contain identifying information on those individuals buried here.