Tentera Laut Rakyat telah dipimpin oleh Kommando der Volksmarine (Markas Tentera Laut) di Rostock-Gehlsdorf. Ia telah disusun seperti berikut (tahun 1985):

• 1st Flotilla in Peenemünde,
• 4th Flotilla in Rostock-Warnemünde,
• 6th Flotilla at Bug on Rügen Island,
• 6th Border Brigade (Coast) in Rostock.

Terdapat tambahan seperti berikut:

• one Torpedo Technical Support Company (TTK-18) in Sassnitz (servicing anti-submarine torpedoes)
• one Naval Helicopter Wing (MHG-18) in Parow near Stralsund
• one Naval Flight Wing (MFG-28) in Laage
• one Navy Engineering Battalion (MPiB-18) in Sassnitz
• one Combat Swimmer Command (KSK-18) in Kühlungsborn
• one Coastal Missile Regiment (Ground Support) (KRR-18) in Schwarzenpfost
• one Coastal Defense Regiment (Ground Support) (KVR-18) in Rostock(from 1988)
• one Naval Propaganda Company (PRK-18) in Rostock-Warnemünde
• the Maritime Hydrographic Service of the GDR (SHD) in Rostock
• testing and other special facilities
• training facilities
  • Naval NCO Academy "Walter Steffens" in Parow (naval training of NCOs and seamen)
  • Naval Officers Academy "Karl Liebknecht" in Stralsund (training of naval officers)
  • NCO School for Support Services at Dänholm near Stralsund (technical training of NCOs)