Thousands of organic micropollutants and their transformation products can be found in water. Although most of them are present at low concentrations, individual compounds contribute to mixture effects and this overall effect is a still a significant public concern. Traditional chemical identification and monitoring of those micropollutants or their products is pain staking and full of challenges. More recently, a battery of cell-based bioassays that target health-relevant biological endpoints are used to assess the water quality to complement chemical analysis. However, the bioassay methods are not cost-effective and lack of significance of systems biology. The objective of this study is to evaluate the suitability of metabolomics technology to benchmark water quality and to assess efficacy of water treatment processes. In details, cell-based (MCF7) metabolomics method is used to assess a set of 8 water samples collected in Australia, including wastewater treatment plant effluent, two types of recycled water (reverse osmosis and ozonation/activated carbon filtration), stormwater, surface water, and drinking water. The result showed that many of critical metabolic pathways has been altered in the water samples and there is great difference between treatments. Among them, filtration has the most effective removal of the toxicity. This study has preliminarily demonstrated that cell-based metabolomics method are sensitive to benchmark water quality and could be potentially used in the risk assessment in the future.