The exterior is rubble limestone quarried in the downriver area and brought upstream by barge. The trim is Kelly Island sandstone. The north and south side walls and roof are supported by buttresses and hammer beam trusses. The tower and belfry rise 105 feet and the building, including the chapel, is 170 feet long and 65 feet wide. A large number of gargoyles may be seen in the roof lines and in the base of the hood moldings of the windows and doors.
Gargoyles are common to early European church structures where they serve as downspouts.
The nave of St. John's is entered from the narthex through a Caen stone archway and oak doors erected in memory of Henry Porter Baldwin II, who like his uncle, gave generously of his means and talents to the church. Two major changes have been made in the interior since the church was built. Originally, the chancel was shallow and the organ and choir were located in the west gallery. In 1892, the chancel was deepened ten feet to provide space for the organ console and a chancel choir of 50 men and boys. To permit this, the chapel was taken down and rebuilt 10 feet to the east.