Abstract The East China Sea continental shelf offshore from the Yangtze River estuary is a sedimentary system characterized by complicated hydrodynamic conditions and large variability in sediment texture. Granulometric, geochemical and environmental magnetic analyses were carried out on surface sediments from this area to investigate the spatial variations of sediment composition and their underlying mechanisms. Magnetic properties of three particle-size fractions (< 16 µm, 16–63 µm, > 63 µm) were further analyzed to assist data interpretation. Our results reveal four distinct units: subaqueous Yangtze delta and inner-shelf mud deposits (Unit A), relict sands on the middle shelf (Unit B), the transitional environment between Unit A and B (Unit C), and the area northern to Unit A (Unit D). The distributions of organic carbon, iron, manganese and their ratios (Mn/Fe) suggest minor effects of reductive diagenesis on the surface sediment magnetic properties. Because of differences in sediment source and hydrodynamic conditions, sediments in Unit A have the highest ferrimagnetic and antiferromagnetic mineral concentrations, as well as the finest ferrimagnetic grain size. The significant variations of magnetic properties within Unit A indicate the effect of particle size sorting during sediment transportation and deposition. Sediments in Unit B have the coarsest ferrimagnetic grain size and the highest proportion of ferrimagnetic versus antiferromagentic minerals. Unit C, which has a bimodal size distribution, can be subdivided into a southern and northern part magnetically, reflecting the influence of provenance and particle size. The distinct magnetic characteristics of Unit D are probably due to the strong influence of materials from the Yellow River. Our results provide a new method for characterizing East China Sea shelf sediments offshore of the Yangtze River mouth, against which the extent of the influence of the Yangtze River on the East China Sea can be examined. Furthermore, it may provide a baseline for future long-term monitoring in this sensitive continental-margin environment that is influenced by the Yangtze River.