The Navy was made up of two big tactical units: the Sea Division and the Danube Division. There were also the smaller "Sulina" Naval Detachment and the Upper Danube Sector.

The Sea Division had the mission to defend the coast line from any enemy attack. It consisted in the Sea Naval Force, the “Constanta” Harbour Area Command, the “Constanta” Coastal Artillery Group (6 batteries), the Seaplane Flotilla (3 squadrons with 20 airplanes in total), the Naval Equipment and Materials Storehouses, the Service Group and the sedentary part of the Coastal Artillery Regiment.

The Sea Naval Force was made up of:

• the Destroyer Squadron: 4 ships
• the Gunboat Section: 3 ships
• the Corvette Section: 3 ships
• the Mine-laying Section: 5 ships
• the Submarine and Torpedo Boats Group: 1+3 ships

The Danube Division had the mission to defend the Romanian part of the river. It consisted in:

• the River Naval Force:
• the Monitor Squadron: 3 ships
• the Torpedo Boat Section: 2 ships
• the Landing Company
• the Underwater Defence Group
• the Service Group
• the "Tulcea" Tactical Group:
• the River Group: 2 monitors and 4 torpedo boats
• the Underwater Defence Sector
• the Supply Convoy

The "Sulina" Naval Detachment had the mission to secure the defence of the Danube Delta. It had three smaller detachments: "Sulina", "Periprava" and "Chilia Veche" and the Patrol Boat Section.

The Upper Danube Sector had the mission to defend the line along the river from Cazane to Portile-de-Fier. It was made up of 2 artillery batteries, a search-light section, a river boat section (2 ships), the sedentary part of the Marine Regiment and of the Navy Engineer Regiment.

On 22 June 1941, the navy had at its disposal 40 main military ships: 23 on the Black Sea and 17 on the Danube. The 4 destroyers (NMS Regele Ferdinand, NMS Regina Maria, NMS Marasesti and NMS Marasti) were the most important Romanian warships, but only the first two were newer (1928-29). The NMS Delfinul submarine was launched in 1936. The 3 corvettes (NMS Naluca, NMS Smeul and NMS Sborul) and the 3 gunboats (NMS Ghiculescu, NMS Stihi and NMS Dumitrescu) were built before WWI. The 3 torpedo boats (NMS Viforul, NMS Vijelia and NMS Viscolul) and the NMS Amiral Murgescu mine-laying ship were the most modern ships (from 1939).

On the Danube, the main warships were the 7 monitors (NMS Kogalniceanu, NMS Bratianu, NMS Lahovari, NMS Catargiu, NMS Basarabia, NMS Bucovina, NMS Ardeal). The first four were built in 1907 and the other three shortly before WWI. There were also 4 torpedo boats built in 1907, two armoured patrol boats and 5 riverboats imported from Czechoslovakia in 1940-41.

The Navy had requisitioned many ships (cargo-boats, tugs, oil tankers etc.) from the Romanian Maritime Service, the "Steaua Romana" company, the Romanian River Navigation company and others.

The Soviet Black Sea Fleet was much more powerful than the Romanian Sea Naval Force. This is why the Romanian Navy executed only convoying, mine-laying and coastal defence missions.

The German naval presence in the area wasn't too important until October 1942. The naval operations were coordinated by the German Black Sea Admiral ("Admiral Schwarze Meer"), based in Varna, Bulgaria.

From the outbreak of war until August 1944 the navy increased the number of ships and troops it had. The Sea Division received 6 new torpedo boats built at Galati under license from the Dutch (Power class), 2 submarines (NMS Rechinul and NMS Marsuinul), built also at Galati Under Dutch/German license (IA U-boot), 5 small Italian CB subs, 3 German KFK submarine hunters, 3 motor transport pontoons, 8 tugs. The Danube Division received an armoured patrol boat (captured Soviet gunboat), 5 anti-magnetic mines tugs, 7 patrol boats and 6 tugs. Also many other civilian ships were requisitioned.

In the autumn of 1941, the navy was reorganized. The "Liman" Naval Detachment and "Odessa" naval Detachment were created, with a structure similar to the "Sulina" Detachment. The Sea Naval Force was now a larger formation. It subordinated directly to the Navy Command. Its place in the Sea Division was taken by the "Sulina" Naval Detachment.

In 1943, the Submarine and Torpedo Boats Group was divided into the Submarine Squadron (3 ships) and the Torpedo Boat Squadron (7 ships).

The River Dredging Flotilla was created inside the Danube Division. The monitors were reunited in the Monitor Flotilla and to defend the Danube downstream from Calafat the Middle Danube Sector was created.

Between 1943-44 new artillery pieces were imported from Germany and Italy and new coastal batteries were installed along the coast line. The most important were near Constanta and Mangalia. Near the Constanta harbour was also the German "Tirpitz" battery, which had 3x280 mm guns and a lot of AA artillery around it.

On 19 August, a day before the Soviet offensive started the Navy had 54 ships on the Black Sea (29 warships and 25 auxiliary) and 137 on the Danube (37 warships and 100 auxiliary), a marine regiment, a navy engineers regiment and a coastal artillery regiment.

The last reorganization of the Romanian Royal Navy took place after 5 September 1944. The main sea warships were given to the Soviets, who interned them in the Caucasus ports. The river warships were also taken by the Soviets and fought until the end of the war. There were now 3 commands: the Sea Naval Force Command, the Coastal Command and the River Forces Command, and 3 detachments: the Lower Danube Detachment, the Middle Danube Detachment and the Upper Danube Detachment.