The Cao'e River is located in the Qiantang River estuary. The sedimentation and provenance of the river were complicated under the effect of the Qiantang River tide before the estuary sluice was built in December 2008. XRD and environmental magnetism are adopted as means to study clay mineralogy of the surface sediments and their spatial distribution in this paper, with emphasis on the sources of clay minerals in the mainstream and the influence of estuary sluice on sedimentation after construction. Results show that the clay mineral assemblages in tributaries are rather similar to those in topsoil sediments, in which the 1.4nm clay minerals are dominated by vermiculite and 1.4nm mixed layer clays. In the mainstream, however, the contents of 1.4nm clay minerals vary at different river sections. For examples, vermiculite dominates the 1.4nm clay minerals in the upper reach before the Shangpu gate, chlorite in the lower reaches of the New Sanjiang gate, and two 1.4nm clay minerals (chlorite and vermiculite) in the section between the Shangpu gate and the New Sanjiang gate. With regard to the magnetic properties of the sediments, they are similar among topsoil, tributaries and the upper reach sediments of the Shangpu gate. The magnetic properties of sediments' in the lower reaches of the New Sanjiang Gate is similar to that offshore. Magnetic properties of sediments between the Shangpu gate and New Sanjiang gate vary in between. The study of sediment source shows that the sediments of the mainstream above the Shangpu gate comes from tributaries and topsoils; sediments of the lower reaches of the New Sanjiang Gate from the Yangtze River, Hangzhou Bay and Qiantang River; and the sediments between the Shangpu gate and New Sanjiang gate from tributaries and topsoils with strong influence of materials from the outside of the River.