The 89-year-old monarch and her husband Prince Philip were aboard the "Maryanne", a boat from the early 1950s and the period when the couple had called the Mediterranean island home.
The trip on the dghajsa -- a traditional water taxi -- was the highlight of a nostalgic day, which saw the royals return to several of their favourite haunts from their youth.
Dressed in a bright turquoise A-line coat, the queen held her hat on in the wind as the red, yellow and green-striped boat, with the royal standard flying from its stern, sailed towards Britain's HMS Bulwark assault ship, which was adorned with colourful signalling flags.
It was reportedly the happiest time of their lives and the pair have returned several times over the years -- most recently in 2007 to celebrate their diamond wedding anniversary.
"Visiting Malta is always very special for me. I remember happy days here with Prince Philip when we were first married," the queen said in a speech before the boat ride.
On their return in 2007, which was dubbed a "second honeymoon", "we could not help but be impressed by the progress and the sense of optimism" in Malta, she said.
As the cannons fired from the Barrakka gardens on the sea front -- where Elizabeth, then in her early 20s, used to come and wave in the navy fleet -- the crew of the HMS Bulwark performed a royal salute, holding their caps aloft and cheering "hip hip hooray!".
Security was heavy, with snipers on the rooftops and four patrol boats with armed sailors circling the bay for the ride, which wound up a three-day state visit that began Thursday.
Earlier, the couple had visited the Heritage Malta centre which conserves the country's historical sites, including ancient temples which folklore has it were built by giants.
The centre is in the former Bighi Hospital -- a major navy infirmary that served a vast area from 1832 until 1970, giving Malta the nickname "The Nurse of the Mediterranean".
It was a hugely independent time for the future queen, who used to beetle around the island in her own car and enjoyed shopping, partying and spending the day at the races.
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