1st, 2nd, and 3rd Squadrons contain the main part of the navy and are based at the naval bases in Frederikshavn and Korsør.

1st Squadron is primarily focused on national operations in and around the Faroe Islands and Greenland.

2nd Squadron is mainly dedicated to international operations and focused on combat operations.

3rd Squadron is primarily tasked with national operations, maritime surveillance, maintaining sovereignty, and support to civilian society.

The vessels and crews that the Royal Danish Navy can deploy in international operations are primarily drawn from 2nd Squadron, although units from 1st and 3rd Squadrons may also be deployed, and have been in the past.

1st Squadron

4 multi-role frigates (THETIS class)
3 Arctic patrol ships (KNUD RASMUSSEN class)
The Royal Yacht (HDMS Dannebrog)

2nd Squadron

3 frigates (IVER HUITFELDT class)
2 ASW frigates (ABSALON class)
6 patrol vessels (DIANA class)
Modular mine-clearing assets under MCM Denmark

3rd Squadron

2 environmental-protection vessels (GUNNAR THORSON class)
2 environmental-protection vessels (METTE MILJØ class)
3 environmental-protection craft (MILJØ 101 class)
2 training boats (HOLM class)
2 hydrographical survey craft (HOLM class)
1 support ship (HDMS SLEIPNER)
2 sailing yachts (HDMS SVANEN and HDMS THYRA)