Microbial and inorganic fouling can pose major challenges in operations of groundwater remediation system extraction and treatment. Pipeline and unit operations biological fouling can lead to process upsets through reduced extraction rates, system fouling, reduced operating time, and increased maintenance costs. Extraction and discharge conditions may provide scenarios under which it is advantageous to consider treatment options that reduce disinfection by-product formation, are effective through non-oxidative pathways, mitigate inorganic deposition, and are effective in pre-treatment or early treatment stages. Two pilot tests were conducted to determine the efficacy and fate of two biological control agents (non-oxidizing and oxidizing) and five inorganic deposit control agents. The two biological control agents included: Tetrakis (hydroxymethyl) phosphonium sulfate (THPS – non-oxidative) and peracetic acid (PAA - oxidizing). The five deposit control agents included: Ethylenediaminetetraacetic acid (EDTA), citric acid, a terpolymer, Etidronic acid (HEDP), and sodium metasilicate. Groundwater from two aquifer units were tested with differing properties (microbial communities, ORP, and inorganic compounds). Results of the pilot tests for the biocides provided insights into the differing microbial community control efficacies, demand in differing groundwater conditions, and fate in groundwater treatment unit processes (oxidant media, advanced oxidation process, carbon filters, and reverse osmosis). Results of the pilot tests for the deposit control agents provided insights into chelation/complexation with the oxidative biocide PAA, efficacy in reducing inorganic oxidation from the biocide PAA, and fate in groundwater treatment unit processes. Results can assist designers and engineers that are investigating methods in mitigating microbial fouling and inorganic deposit formation in operations of groundwater remediation system extraction and treatment.