The fortress was founded in 1701 by order of Tsar Peter I to protect the Arkhangelsk fairway in anticipation of a Swedish attack during the Northern War of 1700-1721. The project was developed by German engineer Georg-Ernest Reze. It was considered one of the best fortresses in Russia.

The fortifications included a square four-bastion citadel and external defenses: a fosse, a moat, a ravelin, a covered way, a palisade, and a glacis. Inside the citadel, two brick buildings were constructed for the commandant and senior officers, four powder magazines, barracks, military ammunition storages, and a tower with a flagpole. In the central square stood a wooden church of St. Peter and Paul.

Major construction work was completed in 1705, and the final formation of the complex occurred in 1714 with the completion of the ravelin on the northern side of the fortress.

During the Crimean War (1853-1856), the fortress did not participate in combat, but its location on the way to Arkhangelsk disrupted the plans of the Anglo-French squadron's attack. The enemy did not dare to enter the mouth of the Northern Dvina, fearing the fire from the fortress's cannons. The fortress was abolished in 1863 and transferred to the Arkhangelsk diocese.

In Soviet times, the territory of the fortress first housed a children's colony-commune, then a correctional labor institution, which existed until 2006. In December 2007, Novodvinsk Fortress was handed over to the Arkhangelsk Regional Museum of Local Lore and received the status of a federal heritage site. Since 2008, emergency repair work has been carried out on the fortress grounds. Currently, the southern and western parts of the citadel with two main gates are in relatively good condition; other fortifications have only partially survived.