In preparation for the Israeli War of Independence, its role was defined as the creation of coastal bridgeheads and transport of supplies to isolated settlements.

Before the Israeli War of Independence the Palmach submitted a proposal to David Ben-Gurion in which the duties of the Israeli Navy were defined including amphibious assaults, reinforcement of operations, protection of coastal settlements, transportation of landing troops and vehicles, supply of fuel and equipment were included for which a specialised landing unit "Shayetet 11" was established.

[9] During the war, Nahariya was cut off from the rest of Israeli territory so the supply of troops and equipment to the isolated area was carried out by sea.

The naval force of the Flotilla (transporting 22nd battalion of Carmeli Brigade) landed at 02:30 on the beach of Shebi Zion and began to attack the village of Samaria from the north.

[13] During the Operation Death to the Invader Israel Defense Forces attacked Beit 'Affa by a company of the Flotilla and 54th battalion of the Givati Brigade.

The naval unit advanced through a wadi from the north, hoping to surprise the Egyptians, but were in fact spotted while preparing to set up.

The complex operation involved a two-column attack from the north and south, which included both infantry and armored vehicles, as well as an amphibious assault conducted by troops of the Flotilla who crossed the sea by boat.

During the Battle of the Chinese Farm Matt's brigade began moving to Tasa at 4:30 pm on October 15, before turning eastwards on Akavish.

[23] During Operation Raviv "Pinko" Harel's small force of about a hundred men, six Tiran 5s and three BTR-50s, landed on the Egyptian coast at 03:37AM on the morning of September 9.

[24] Laden with extra fuel and ammunition supplied by the Flotilla, the force headed south, wreaking havoc behind Egyptian lines and attacking installations along the way.

[28] During the Operation Abirey-Halev, On the night of 15 October, 750 personnel of Colonel Matt's 55th Paratroopers Brigade crossed the canal in rubber dinghies.

On June 6, 1982, Israeli forces under direction of Defense Minister Ariel Sharon launched a three-pronged invasion of southern Lebanon in "Operation Peace for Galilee".

Roughly 60,000 troops and more than 800 tanks, heavily supported by aircraft, attack helicopters, artillery, and missile boats, crossed the Israel–Lebanon border in three areas.

[34] An Israeli amphibious operation was conducted north of Sidon, beginning with a diversionary bombardment of targets away from the landing zone by missile boats and aircraft.

In August 1993 all of flotilla vessels were taken out of service as they were deemed vulnerable and State-of-the-art fast landing craft were not defined as an operational necessity.