Mercury is a pervasive and harmful heavy metal element in the natural environment, and it is also one of the most important indexes of heavy metal detection in water. As a kind of trace analysis technology, hydride generation-atomic fluorescence spectrometry(HG-AFS) has been widely applied because of its advantages such as simple operation, high degree of automation, high sensitivity and little influence of human factors. The contents of mercury in four important water areas around Qujing City were determined by hydride generation-atomic fluorescence spectrometry, the results show that the mercury contents of the measured waters vary little and are all within the limits of safety. This research not only has a certain significance for the water environment status in Qujing City, but also develops a rapid method for detection of trace mercury in water.