The entire hospital complex is listed on the National Register of Historic Places along with the rest of the Navy Yard.

However, its facilities were described as inadequate; an 1811 letter described the hospital as being in a pond that flooded during high tide, and without any sterile lining to prevent disease transmission.

[4] At the time the hospital was constructed, the area was still largely rural, and its buildings secluded from the developed sections of Brooklyn.

[4][10][11] Shortly afterward, when the American Civil War broke out, Squibb provided drugs to the Naval Hospital from his laboratory on nearby Furman Street.

[7] By the end of the 19th century, the mud flats separating the hospital and the rest of the Brooklyn Navy Yard were filled in and developed.

[14] By 1913, the quarters for the officer in command of the medical supply depot was being converted into a facility for patients with contagious diseases.

[1] These improvements, along with four additional buildings that no longer exist, allowed the hospital to accommodate 3,000 patients at a time during World War I.

[7][19] In preparation for World War II, the Works Progress Administration refurbished the Naval Hospital's 37 buildings, although no new structures were built.

[19] The Brooklyn branch of the Red Cross Service, also helped the hospital's patients with rehabilitation activities.

[31] The hospital, along with the rest of the Navy Yard, was listed on the National Register of Historic Places (NRHP) in 2014.

[32] The Steiner Studios plan calls for the restoration of 15 NRHP-listed buildings at the Brooklyn Naval Hospital campus, but would also demolish some of the NRHP-contributing artifacts to make way for the new facility.

[33] Structures with a total floor area of 2,700 square feet (250 m2) would be demolished and replaced with landscaped lawn space.

[36][6][1] The long side of the "E" contains a symmetrical portico recessed into the walls and surrounded by eight 2-story-tall stone Doric piers.

[27][36] The building was cited as a "rare surviving example of early institutional design" in the city's landmark report.

[39] A two-story Surgeon's House (Building R1),[35] designed in the French Second Empire style, was built in 1863 by builder True W. Rollins and civil engineer Charles Hastings.

[14][6] The entrance to the house is symmetrical and contains a small pair of steps to a large doorway, with segmental arches and balustrades on either side of the entryway.

It contained two garage slots on the first floor, and a second story with rectangular windows and stone windowsills with flush lintels.

There are segmental arched windows on the longer elevations of the building, as well as a garage with sliding wooden doors on the southern side.

A two-story wing is attached to the north facade and contains an entrance with segmental arches, as well as rectangular windows.

A balcony runs along all three stories on the west side the building and was constructed around 1947; it contains one-over-one windows with metal frames.