The basin that holds the Zoo and the Birmingham Botanical Gardens lies south of Red Mountain and north of Shades Mountain. Fresh spring water from under the zoo once provided water for fish hatchery ponds built from Hartselle Sandstone.
A small unnamed creek drains through the Zoo. The creek joins Watkins Brook flowing out of the Country Club of Birmingham and makes its way into Shades Creek. The creek is one of the major tributaries to the upper Cahaba River, joining it where the river crosses from Shelby into Bibb County 26 miles to the southwest. The Cahaba watershed, the only free-flowing river of its size in the state, is famous as one of the most biologically rich rivers in all of North America, hosting over 130 fish species and dozens of rare and endangered mussel, snail, and crayfish species. The Cahaba is also the source for about 25% of Alabama’s drinking water, with much of that going to the Birmingham metropolitan area. The river ends when it joins the Alabama River near Selma, AL. The Alabama and many other major watersheds of the state are part of the Mobile River Basin. Thus, rainwater falling on the Zoo can wind up in the Gulf of Mexico.