At the beginning of the Romanian–German invasion of the Soviet Union on June 22, 1941, the Flotilla cooperated with Red Army troops in the defense of the southern front. On June 24–25, 1941, the Flotilla participated in a counterattack crossing of the Danube onto the Romanian side. After this, the Flotilla supported troops trapped in bridgeheads, and as the Red Army withdrew to Odessa the Flotilla ferried troops across the Southern Bug and Dnieper Rivers.