For thousands of years, the Coast Salish people inhabited the Saanich Peninsula. This region was used for hunting, fishing and collecting plants. Camas bulbs were eaten as root vegetables; cat-tail leaves were used to weave baskets; licorice ferns were gathered for cold remedies; and cottonwood gum made excellent waterproofing for baskets. According to reports in the 1858 Victoria Gazette, hunters were shooting two or three elk per day near Elk Lake. Elk/Beaver Lake was previously two separate water bodies isolated by land. Beaver Lake was a shallow marsh created by beaver dams. In 1872, Elk Lake became the water source for Greater Victoria. Elk and Beaver Lakes were joined when Colquitz Creek was dammed at the south end of Beaver Lake. The lake area and depth was expanded between 1873 and 1879 in order to supply drinking water to the growing population of the City of Victoria. The lake surface area was expanded by 21% (from 1.84 to 2.24 km2). This effort also expanded the shoreline perimeter by 19%. In 1896, filter beds were constructed after Victoria residents complained of fish and tadpoles in their drinking water. The lake provided water to the residents of Victoria until 1914, and remained a water source for some areas of the region until 1977.

The CRD upgraded the Beaver Lake dam in the summer of 2014. The new dam better regulates water release to the Colquitz River, which is essential to maintaining fish habitat during the summer and controlling water release in the winter. The dam upgrade includes a fish-passage ladder and a new spillway. A new pedestrian bridge was installed below the spillway to allow continued use of the Beaver Lake shoreline trail.

Although there is no information to indicate the natural state of the lake prior to human settlement, paleolimnological data indicate that the rate that sediment was moving into the lake was increasing before the middle of the 19th century, and increased exponentially after that up to at least 2000. This is a common consequence of land clearing, agricultural activities, and increasing the area of impervious surfaces and increasing use of fertilizers, all of which have occurred in the Elk/Beaver Lake watershed, with the most intense development occurring after the 1950s. Water quality monitoring found the first signs of high nutrient levels (high productivity) in Elk/Beaver Lake in 1968, and the lake was concluded to be highly eutrophic (high in nutrients) by 1972.

Elk Lake has been a key recreational resource for many decades. From the 1920s through the 1940s the lake was the focus of resort and water-based recreation. Elk/Beaver Lake was established as a regional park in 1966 and is a very high value community resource for recreation (swimming, boating, rowing), fishing, and general sightseeing and enjoyment. The lakes are stocked by the Ministry of Forests, Lands, and Natural Resource Operations with approximately 18,000 rainbow trout each year. A 10 km walking/running path around the lake is heavily used. The portion of the path on the west side of Elk Lake is open to bicycles and horses. CRD estimates that Elk/Beaver Lake Regional Park receives 1.5 million visitors per year (2015). The lake hosts two major triathlons, and is currently host to the Canadian National Rowing Team. Rowing Canada has plans to establish a permanent national training centre in North Cowichan at Quamichan Lake by October 2020. However, significant local rowing activity will continue at Elk/Beaver Lake in the future.