When DND acquired the former Yarrow’s Shipyard site in 1996, much of the area had been capped with gravel, and most infrastructure either removed or buried. DND removed most known contaminated surface soils in 2000, and monitoring wells were installed around the site. In 2005, high contamination levels in some of the wells prompted development of a remediation plan for the site. Work began in 2008 and was completed in 2009, involving construction of a specialized concrete barrier wall around the site, and removal and replacement of 40,000m3 (over 100,000mt) of contaminated soils. The former shipyard site is now used for parking and storage of small boats and ship repair materials.
Several other land and marine based remediation projects have been conducted around the harbour in recent years. One such project was remediation of the former Colwood Fire Fighter Training Area near Paterson Point, where training in damage control and firefighting has been conducted since the 1950s. When this facility was replaced with a safer, cleaner indoor facility, the old site was remediated in 2005 and part of the site re-naturalized with native vegetation.
In January 2013, the Department of National Defence created three nearshore underwater reefs in Esquimalt Harbour, two adjacent to Fort Rodd Hill National Park, and one just south of Duntze Head on the east side of the harbour entrance. Each is about 20 m x 40 m and composed of large boulders. This marine life enhancement project is designed to offset any future sub-marine works that the DND may undertake near their jetties or other structures in the harbour. It is estimated that the reefs will create about 11,000 m2 of rocky reef habitat, providing substrate and cover for invertebrates, seaweeds and fish.