Objectives To investigate the status of microbial contamination in drinking water from rural centralized water supplies in Hezhou and explore relevant prevention measures to provide scientific basis for improving water quality from rural centralized water supplies.

Methods Microbiological indicators were tested for 1 716 water samples collected in 2012-2016 from 429 rural centralized water supply projects in Hezhou according to the method of (Standard examination method for drinking water) GB/T 5750-2006. The result of microbiological indicators in water samples under different condition were analyzed statistically.

Results The qualified rate of all microbiological indicators in 1 716 water samples was 35.90%, which was statistically different among centralized water supplies with different water treatment processes and from various water source types (P < 0.001). The qualified rate of central supplied water based on microbiological indicators was irregular in Hezhou in 2012-2016.

Conclusions The qualified rate of central supplied water based on microbiological indicators was related to water source type and treatment process. It suggests that in order to improve the quality of rural central supplied water, especially the qualification rate of microbiological index, improving the purification and disinfection technology and facilities, strengthening the hygienic protection of water sources, and promoting health education in rural areas were needed to guarantee the safety of drinking water for rural residents.