Abstract: A process for constructing a soil-based rhizosphere flow-through system to break down contaminants in contaminated water. The process includes the steps of: providing plants planted in soil in a test bioreactor, the plants providing a rhizosphere; exposing the rhizosphere to the contaminated water; extracting microorganisms from the rhizosphere following their exposure to the contaminated water; preparing a microbial suspension from the extract; subjecting the microbial suspension to growth conditions to increase the concentration of the microorganisms, thereby preparing a soil conditioner; adding the soil conditioner to soil in a contained area having a water flow inlet and outlet; and planting a plurality of plants in the soil, the plants being of the same species as the plants of the test bioreactor.