The Western Naval Command HQ is located at Apapa in Lagos. It covers the sea and coastal areas from the Nigeria/Benin border at Long 002o 49’ E to Long 006o E in Delta State from the Nigerian coastline to the limit of the nation’s EEZ.

The Command has the following units under its jurisdiction:
1. Western Fleet at Apapa.
2. NNS BEECROFT, an operations base at Apapa.
3. Naval Air Station, Ojo, Lagos.
4. Nigerian Navy Reference Hospital, Ojo, Lagos.
5. Fleet Support Group (West) at Apapa.
6. NNS WEY, a maintenance unit at Navy Town, Ojo.
7. Forward Operating Bases (FOB) IGBOKODA  in Ondo State.
8. Nigerian Navy Secondary School, Abeokuta.
9. Nigerian Navy Secondary School, Ojo.
10. Forward Operating Bases (FOB) BADAGARY and TAKWA BAY in Lagos