Karst water has been served as a vital drinking water source for approximately a quarter of the global population. Due to the development of cities and the accompanying drinking water usage, the assessments of heavy metal pollution in these karst waters have become relevant. Therefore, this study assessed the heavy metal (Cr, Mn, Co, Ni, Cu, As, Cd, and Pb) pollution levels and water quality characteristics of in sixteen water samples, which were collected from three typical karst reservoirs in Guangxi Zhuang Autonomous Region, Southwest China, including Guishi Reservoir, Lingdong Reservoir, and Lingshui Lake. We also analyzed the possible sources of heavy metals in water and evaluated the ecological risks caused by these compounds using heavy metal pollution index (HPI), heavy metal evaluation index (HEI), while hazard quotient (HQ) was used to assess human health risk due to the use of these waters. The result showed that Manganese (Mn) contents in Sites G-K1 (Guishi Reservoir) and LD-K7 (Lingdong Reservoir) were high than others, with values of 110.93 and 159.25 μg/L, respectively, which exceeded the value of 100 μg/L specified in China’s Surface Environmental Quality Standards for Surface Water (GB3838-2002). However, the calculation results of HPI (low pollution, ˂15), HEI (low pollution, ˂10), and HQ (no health risks, <1) of all water samples showed that these reservoirs were not polluted by heavy metals and showed no risk to human health. The heavy metals detected in these regions primarily originated from the natural environment, while the exceedance of Mn concentrations in some areas may have been influenced by surrounding anthropogenic activities. Additionally, our findings may aid in comprehending the behavior of heavy metals in typical karst reservoir water under human activity’s influence.