A simple and rapid method has been developed for the determination of total Hg in drainage sediment. The method is performed by using a sequential injection (SI) system with cold vapor generation atomic fluorescence spectrometry (CVAFS) after a closed microwave assisted digestion. Digestion was carried out at a temperature of 140°C for 5 minutes using a mixture of 10% HCl + 50% HNO3 +40% H2O as digestion acid media. Stability experiment revealed that the extracted samples were stable in 24 hours. The SI–CVAFS system was well optimized. At optimized conditions, the detection limit of the method was 0.5 ng/g−1. Relative standard deviation (RSD) for the complete procedure by the analysis of the 10 digestions was 3.7%. The method was validated against 3 drainage sediment certified reference materials: GSD-2, GSD-9, and GSD-10 and successfully applied to the determination of Hg in the sediment of Pi River, China.