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Groundwater is found in aquifers, which are underground formations of permeable or fractured bedrock or unconsolidated sediments that can produce useful quantities of water when tapped by a well. Sand and gravel aquifers generally yield much greater amounts of water than do bedrock aquifers because of their larger holding capacity. Water in aquifers is replenished, or recharged, from rain, snowmelt, lakes and rivers.

Much of the population outside of Victoria and Nanaimo obtains its water from highly productive sand and gravel aquifers. Some of the more mountainous regions and the Gulf Islands have mostly bedrock aquifers which are less productive. Though a few wells drilled in bedrock aquifers on southern Vancouver Island supply sufficient quantities of water to irrigate farmland, most bedrock wells yield only enough water to meet the needs of a single family.

One of the largest sand and gravel reservoirs on southern Vancouver Island is in the lower Cowichan River valley. Wells drilled into this aquifer provide sufficient water for industry, fish hatcheries, pulp mills, agriculture and between 1000 and 1600 homes.

To date, contamination of the Cowichan River has only been a minor issue, however, it is vulnerable to seepage from surface and underground storage facilities and chemical spills. Such contamination would be difficult and costly to rectify, and once affected, the aquifer might be unusable for decades.

On parts of southern Vancouver Island and in the Gulf Islands, the intrusion of salt water into aquifers is becoming a problem. Pumping more fresh water than can be recharged naturally may allow seawater to invade the aquifer. Urbanization, including the construction of paved roads and parking lots also affects groundwater aquifers by not allowing as much surface water to penetrate into the ground and recharge the aquifers.