The work was development and application of the purification system suitable for the treatment of groundwater used for human consumption as well as watering of the plants in the system for the hydroponic cultivation of tomatoes. For that purpose the well water from the 60 m deep water layer situated near the city of Županja (Eastern Croatia) was processed. Most of the measured parameters exceeded upper permissible limit (UPL) for drinking water. The concentrations of the parameters color, turbidity, iron, manganese, arsenic, phosphates, chemical oxygen demand and ammonia were as follows 292±20 mg/PtCo, 21±5 NTU, 1.72±0.34 mg/L, 0.075±0.014 mg/L, 0.074±0.011 mg/L, 10.4±1.7 mg/L, 37±1 mg/L and 1.2±0.1 mg/L, respectively. Due to the complex composition of the treated water, the purification system required the combination of electrochemical treatment, using iron and aluminum electrode plates with simultaneous ozonation followed by post treatment with hydrogen peroxide and ozone. The electrocoagulation/ozonation approach was used for the removal of heavy metals, color, turbidity, phosphates and partially organic matter while the rest of the organic contaminants and ammonia were removed by the treatment with hydrogen peroxide and ozone. Following the combined electrochemical treatment and post treatment with hydrogen peroxide and ozone all measured parameters in the treated water were in agreement with regulated values. The combined treatment resulted in total removal of arsenic, color, turbidity, ammonia and organic contaminants while the removal of other parameters of interest was up to 97.98%.