HMCS Windsor began the three-hour process of re-entering the water just before 9 a.m. local time in a berth lined with 46 winches that connected to a submerged wooden platform.
Dozens of workers stood on a Halifax dock to watch the hulking black sub as it was lowered at about half-a-metre per minute.
The sub was to move to a neighbouring berth to undergo further testing and preparations for sea trials, but it's not clear when those trials will happen.
"The submarine will only go on the other side and ... the refit will continue," said Roger Barakett, who oversees fleet safety and the lowering procedure.
"Some of the work requires salt water to be carried out so that's what's going to go on when she's in the water."
Initially scheduled to be completed by 2009, Windsor's refit has taken almost five years and the sub hasn't been in the water since 2007. It has operated at sea for 332 days since arriving in Nova Scotia in October 2001.
Windsor is one of four British submarines bought by the federal government in 1998 for $750 million, but the fleet has seen little time in active service since then.
HMCS Victoria, based on the West Coast, was the first submarine to complete the refit and successfully test-fired torpedoes last month.
Defence Minister Peter MacKay said Tuesday that the Royal Canadian Navy is also expanding the number of submariners it has to 330 from 278 in the coming months.
Three of the vessels are scheduled to be in the water by 2013.
Canada declined the option to purchase British torpedoes along with the submarines. As a result, all four submarines are undergoing extensive weapons system changes to use and launch American made Mark-48 torpedoes that are already in the navy's possession.
In addition to the planned refit, the submarines have been involved in accidents that have further delayed their operational use.
During its voyage to Canada in 2004, HMCS Chicoutimi caught fire after seawater damaged the electrical system, killing Lt. Chris Saunders and leaving the submarine inoperable.
HMCS Victoria recently completed a three-year refit, including repairs to dents in the hull that prevented the ship from doing deepsea dives.
HMCS Corner Brook struck the ocean floor off Vancouver Island during a training exercise in June of last year, causing extensive damage to its fibreglass nose cone. It is currently undergoing repairs.