St. Nicholas Naval Cathedral was built as a "naval regimental church" in the period from 1753 to 1762 on the site of a wooden church designed by architect S. I. Chevakinsky in the style of Elizabethan Baroque. The free-standing four-tiered bell tower completed with a high spire was erected in 1755-1758. The territory adjacent to the cathedral was built up with 1-storey barracks for the servants of the naval department. The stone buildings of the Nikolsky market erected in 1788-1789 have survived to our time.

The Lower St. Nicholas Church is consecrated in the name of St. Nicholas the Wonderworker who is traditionally considered the patron saint of sailing and traveling. The main shrine of the cathedral is named after him — a Greek icon of the XVII century with a particle of relics. In the garden in front of the temple in 1908 the Tsushima obelisk was erected in memory of the crew of the battleship "Emperor Alexander III" who died in the Battle of Tsushima. The money for the monument was collected by sailors and officers of the Guards Crew which included the crew of the battleship. A charitable society with a school, a hospital, an orphanage and a women's almshouse operated at the cathedral since 1870.

St. Nicholas Cathedral is one of the few churches in Saint Petersburg that have never been closed. From 1941 to 1999 it was a principal church of the city. The cathedral has preserved its historical appearance and interiors to this day. About 5 thousand people can be in the temple at the same time.