Human activities and environment change within river basins can be indicated by the dynamic change of concentrations of heavy metals in the river sediments. Flood slackwater deposits (SWD) are deposited from the suspended sediment load in flood flow and preserved after the flood recession. The fine-grained sediments were produced by soil erosion during the season of storm rain and great flood over the river basin. Modern flood SWD were collected along the main stream after two large floodings which occurred during 2010-2011 along the upper Hanjiang River valley. The analytical results showed that the contents of clay(63 μm) was between 7.1% and 65.6%. Clay, fine silt and coarse silt in modern flood SWD gradually increased, while sand decreased along the upper Hanjiang River valley. Average concentrations of heavy metals Co, Cr, Cu, Ni, Pb, Zn, Ba and V were 49.7, 161.7, 31.1, 37.2, 26.1, 87.6, 1007.2, 132.4 mg/kg, respectively. Concentrations of heavy metals, Co, Cr, Ba and V, were significantly higher than floodplain background values in China. Index of geoaccumulation(Igeo) and pollution index(PI) were applied to assess heavy metals in modern flood SWD. The order of pollution elements were Igeo(Co) > Igeo(Cr) > Igeo(Ba) > Igeo(V), whereas Cu, Ni, Pb and Zn belonged to unpolluted. Concentration of heavy metals accumulated in modern flood SWD were defined as the moderately polluted by pollution index in the upper Hanjiang River. Results obtained from the principal component analysis (PCA) were confirmed by the correlation analysis. Heavy metals Co and Cr were mainly enriched in sand, whereas Cu, Ni, Pb, Zn, Ba and V were rich in clay, fine silt and coarse silt. Cluster analysis (CA) showed that the cluster depend on geographical location of sampling sites locating at Ankang plain, north and south side of Hanjiang River. The upstream of Hanjiang River is the water source area for China's Middle Route of the South-to-North Water Division Project. These results provide basic physicochemical data for environmental protection and conservation for soil and water in the upper Hanjiang River valley.