Objective To know the status of drinking water quality detection ability of Centers for Disease Control and Prevention (hereinafter referred to as "CDCs" ) at prefecture and county levels in Anhui province, analyze existing problems and promote the capability building of water quality detection laboratory. Methods Questionnaires were used to investigate the water quality detection ability, detection personnel and relevant detecting instruments of CDCs at prefecture, county and district levels in Anhui province. Results In 2015, passing rates of metrological certification of CDCs at prefecture,county levels were 100%, 72.58% and 21.62% respectively. The average detecting abilities of conventional items, unconventional items and all items of city CDCs were 40.2, 29.1 and 69.2 respectively, with county CDCs-34.1, 1.0, 35.2 and district CDCs-12.7, 0.3, 13.7. Water quality detection laboratory personnel of CDCs at prefecture, county and district levels were 9.2, 4.6 and 2.9 per institution respectively. Major water quality detection instruments of CDCs at prefecture, county and district levels were 18.0, 12.8 and 6.0 respectively. Conclusion Of local CDCs all over the whole province, the passing rate of metrological certification was low, water detection ability was weak, the personnel and instruments were insufficient. Therefore, water quality detection ability should be strengthened.