The geologic units present at Lake Johnson are typical of northeast Florida stratigraphy. The surface material consists of Plio-Pleistocene sand hills. The lakes within these hills define the surficial aquifer system of the region. The natural gamma logs from two wells south of Lake Johnson (Index Map A, wells C-0453 & C-0457) indicate that these sands are present above +28.1 m (90 ft) NGVD on the western side below Lake Johnson and may be missing or only a few feet thick on the eastern section of the lake.

Below the sands, the clay and sandy clay of the Hawthorn Formation can be identified in the gamma logs by the sequence of high peaks between +28.1 m (90 ft) and -21.8 m (-70 ft) NGVD in well C-0453. Most of the imagable area of the seismic profiles is within the Hawthorn Formation. Below -21.8 m (-70 ft), the Eocene carbonates of the Ocala Limestone are identified by the extremely low counts (less than 20 counts per second) on the natural gamma logs. These depths are below the imagable areas of the seismic profiles.