Eliminating organic and inorganic pollutants from water is a worldwide concern. In this study, we applied electrochemical oxidation (EO) and adsorption techniques to eliminate ammonia, phenols, and Mo(VI) from aqueous solutions. We analyzed the first stage (EO) with response surface methodology, where the reaction time (1–3 h), initial contaminant concentration (10–50 mg/L), and pH (3–6) were the three independent factors. Sodium sulfate (as an electrolyte) and Ti/RuO2–IrO2 (as an electrode) were used in the EO system. Based on preliminary experiments, the current and voltage were set to 50 mA and 7 V, respectively. The optimum EO conditions included a reaction time, initial contaminant concentration, and pH of 2.4 h, 27.4 mg/L, and 4.9, respectively. The ammonia, phenols, and Mo elimination efficiencies were 79.4%, 48.0%, and 55.9%, respectively. After treating water under the optimum EO conditions, the solution was transferred to a granular composite adsorbent column containing bentonite, limestone, zeolite, cockleshell, activated carbon, and Portland cement (i.e., BAZLSC), which improved the elimination efficiencies of ammonia, phenols, and molybdenum(VI) to 99.9%. The energy consumption value (8.0 kWh kg−1 N) was detected at the optimum operating conditions.