The siege of Dubrovnik and the associated blockade running operations of the squadron took place from September 1991 until May 1992, during the peak of the fighting in the Croatian War of Independence.

In early 1992, the Dubrovnik area saw fierce fighting while combat operations largely ceased elsewhere in Croatia following the Sarajevo Agreement of 2 January 1992.

[18] Upon formation, squadron was tasked with breaching the Dubrovnik naval blockade and maintaining a route that was instrumental to delivery of materiel necessary to successfully defend the city, including food, fuel, medical supplies, arms and ammunition.

The squadron also transported reinforcements arriving from other parts of Croatia and evacuated wounded out of Dubrovnik, and was a lifeline for the besieged troops and civilian population.

The squadron typically deployed its craft in pairs or threes, sailing as close as possible to the Yugoslav Navy vessels when passing Koločep island to reach relative safety of the Rijeka Dubrovačka inlet, in order to utilize blind spots of naval guns.

[23] At dawn on 31 October 1991, the squadron sailed out of Dubrovnik to meet the Libertas convoy—a fleet of civilian vessels, the largest among them being the Jadrolinija shipping line's Slavija, which was endeavoring to deliver humanitarian aid to the city under siege.

During one of these missions, while sailing back from a trip to Bol on the Croatian island of Brač, she was chased by a Yugoslav gunboat and driven aground on a beach near Babin Kuk, just 2 miles (3.2 kilometres) north of Dubrovnik.

[17][21] Sveti Vlaho was the second vessel used by the Croatian Navy, preceded only by a landing craft designated DJB-103, which was brought into use eight days earlier.

[27] On the 15th anniversary of the arrival of the Libertas convoy in besieged Dubrovnik a celebration was held, but no squadron volunteers were invited to attend.