•Spatial-temporal variations of FC concentration in the Tuojiang River were observed.•Health risks of FC for drinking water were evaluated by QMRA and DALY.•Potential health risks were increasing in the basin especially in upstream areas.•Variation of health risks presumably was associated with regional development. Fecal coliform (FC) indicators are commonly used to evaluate microbial or fecal contamination in surface water. As an important tributary of the Yangtze River in China, the Tuojiang River not only receives polluted water but is also a source of drinking water. Previous studies have reported the presence of conventional chemical pollutants, but the contamination and human health risk of FC in this watershed have usually been ignored. In this study, monthly FC concentration data from 2008 to 2018 were utilized to analyze the spatiotemporal distribution and to assess human health risk for daily drinking water by quantitative microbial risk assessment (QMRA) and disability adjusted life year (DALY) models. The results showed that there were significant monthly variations in the concentrations of FC, and the concentrations in May to August were significantly higher than those in other months. The annual concentration in the whole watershed increased slowly from 2008 to 2018. The annual probability of falling ill (Pill_year) caused by FC upstream, midstream and downstream was 4.30 ± 3.92 × 10−5, 1.38 ± 0.49 × 10−5 and 3.38 ± 2.72 × 10−5, respectively. It was found that 5.82% of the DALY values were greater than the limit of 10−6 per person per year (pppy) and could be defined as high health risk points. A total of 37.3% of samples could be deemed potential risk points whose DALY values were between 10−7 and 10−6 pppy. There were significant spatial differences in FC concentrations and health risk among upstream, midstream, and downstream regions. With the rising health-risk value, the high-risk region has transferred from downstream to upstream since 2015. Furthermore, we found that domestic wastewater and livestock sewerage were deemed to be primary sources of FC in the Tuojiang watershed. Moreover, the increasing health risk faced by the local people in the watershed should receive more attention from the public and government. The results of this study could provide insight into the management of FC pollution and health risks, such as sewage treatment, livestock manure management, and personal dietetic hygiene.