Spatial distribution of heavy metals, arsenic and organic matter in recent sediments in the Hangzhou section of the Grand Canal and their relationships were analyzed. The results showed that the concentrations of heavy metals and organic matters varied widely along the canal, and the average geological accumulation factors decreased in the following orders: organic carbon(2.6), zinc(2.1), cadmium (2.0), copper(1.5), lead(1.1), nitrogen(0.9), mercury (0.8), phosphorus(0.4), arsenic(0.2) and chromium(0). Content of heavy metals and organic carbon in the top 10 cm layer were lower than that of lower layers, except for mercury and organic carbon in the S9 section. Contents of organic carbon in the top 50 cm layer of the mud sediments are significantly higher than those underneath. In the bottom mud layer, there is a concentration peak of the pollutants. In the mud sediments of the canal, cadmium mainly occurred in the Fe and Mn oxide fraction, copper in the organic fraction, lead in the Fe and Mn oxide fraction, and zinc in the carbonate and the Fe and Mn oxide fraction.