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Abstract There is a concern about the increasing prevalence of health problems related to the ingestion of fluoride (F−) in the developing world. Drinking water is one important source of F−, and the concentration of F− needs to be known to ensure the safety of drinking water. In this study, F− levels in drinking water were investigated across Taiyuan in Shanxi Province, China. Spatial-temporal distribution characteristics and potential associated health risks were analyzed using GIS. We collected 485 samples from shallow wells without any defluoridation treatments between 2008 and 2016. After analyzing the samples of F− content we found that mean F− levels of urban areas (0.61 ± 0.39 mg L−1), suburban areas (0.70 ± 0.87 mg L−1) and for all of Taiyuan city (0.63 ± 0.56 mg L−1) were in optimum range based on the recommendation by USEPA. However, individual locations within industrial areas (e.g. Gujiao District) had higher F− levels (1.06 mg L−1). A concerning result showed that 12.37% of tested locations had F− concentrations larger than 1.0 mg L−1. We calculated F− Health Risk Indices (HRIs F) and found that highest were associated with suburban areas, especially in the year 2009 and 2010. However, from 2008 to 2016, overall F− levels and HRIs F of the sampled groundwater in Taiyuan City showed a decreasing trend. HRIs F in suburban areas was higher than urban areas, possible due to the heavily prevalent coal mining industry in those areas. Specific policies should be formulated to address HRIs F. Highlights • F- levels of Taiyuan were in optimum range based on the recommendation by USEPA. • Individual locations within industrial areas had higher F- levels. • HRIs F were calculated and the highest associated with suburban areas. • F- levels and HRIs F of the groundwater in Taiyuan showed a decreasing trend. • HRIs F in suburban areas was higher than urban areas. [ABSTRACT FROM AUTHOR]