Lily Spring has an oval-shaped spring pool 132 ft (40.2 m) by 25 ft (7.6 m) with an average depth of 6 ft (1.8 m). The pool is fed by a series of six vents. Flow is from three fissures on the northeast side of the pool. A bowl shaped depression is located near the center, and two seeps in the limestone bank. The spring pool has a limestone bottom. The water was turbid and slightly tannic during October 2002, though locals report the spring is usually clear with a blue-green hue. The spring run averages 10 ft (3.1 m) wide and 3.5 ft (1.1 m) deep and flows 200 ft (61 m) to enter Santa Fe River from the south. A private residence is situated on the north bank of the pool and a picnic area is to the west. The private land surrounding the spring run and the pool is wooded. Discharge on September 30, 1997 measured 39.69 ft3/s.
From the intersection of US 27 and Main Street in High Springs, drive northwest on US 27 approximately 3.3 miles (5.3 km) to the intersection with CR 138. Turn west (left) onto CR 138 and drive about 2.0 miles (3.2 km) to the intersection with Rum Island Road. Turn south (left) at sign for Rum Island and travel approximately 1.5 miles (2.4 km) to the boat ramp. Launch boat and head approximately 1.1 miles (1.8 km) upriver. Lily Spring enters the Santa Fe River from the south.