Water that falls on land within the Brooker Creek watershed that is not carried away by the creek soaks into the ground and becomes part of the upper Floridan aquifer. An aquifer is the area below the Earth's surface that collects and stores ground water. The Floridan aquifer is the largest and deepest in the state and stretches for 82,000 square miles beneath Florida and parts of Alabama, Georgia and South Carolina.

The sandy soils and sinkholes present throughout the watershed allow water to quickly pass through the upper layers of soil and into the aquifer. The speed at which water is able to soak through surface soil and into the aquifer is known as the aquifer's recharge rate. Most of the groundwater recharge that occurs in Pinellas and Hillsborough counties takes place in the Brooker Creek watershed.

Throughout Florida, approximately 2.5 billion gallons of water are removed from the aquifer each day by houses with wells and by municipal water treatment facilities. Once they remove the water, municipal water treatment facilities treat the water and send it to houses as tap water used for drinking, household activities and outdoor use.

If water is removed from the aquifer more quickly than rain falls to recharge it, the amount of ground water decreases. This decrease reduces the amount of fresh water available to residents, causes lake levels to drop and impacts native plants and wildlife.

Pollutants also threaten aquifer health. The sandy soils present in the Brooker Creek watershed allow water to quickly pass from the surface to the aquifer, but do not thoroughly filter pollutants from the water. Nitrogen and bacteria from surface sources can easily pass into the ground water of the Brooker Creek watershed.