Lake Johnson lies within the Central Lake District physiographic province. It is within the Interlachen Sand Hills subdistrict. The lake is adjacent to the Trail Ridge Sands which is a paleodune ridge that extends north into Georgia. This region includes the largest number of cover collapse sinkholes and provides direct recharge to the underlying Floridan aquifer system. Vegetation that includes longleaf pine and turkey oak is prevalent. Internal drainage through the sinkhole lakes has limited the formation of streams except during periods of high rainfall.

The surficial sands provide storage for rainfall and recharge to the lakes during high water-table conditions. The potentiometric surface of the Floridan aquifer is lower than the lake so a continual downward gradient exists and provides the mechanism for recharge. Pathways for recharge exist where the thick clay and sandy clay units within the Hawthorn Group are breached by collapse sinkholes.