Abstract: There is provided a bio-remediation system and a method associated therewith for remediating a spilled hydrocarbon-based fluid from soil effectively and without causing migration of the fluid to previously uncontaminated areas. The bio-remediation system removes hydrocarbon-based fluid from a subterranean location using microbes which are immersed in a nutrient-rich medium. The microbes biologically remediate the hydrocarbon-based fluid by consuming the hydrocarbon-based fluid. The bio-remediation system ensures that the microbes and the nutrient-rich medium do not extend below the water table thus producing further contamination by monitoring moisture levels and levels of respiratory gases in the soil. When the microbes descend too deep, an air pump is actuated to dry a buffer zone between the water table and the spilled hydrocarbon-based fluid, thus halting progression of the microbes in the nutrient-rich medium.