The Quaternary stratigraphy of the Yangtze delta has been revealed by a deep (344.64 m) continuous borehole, the sediments of which are divided into four sections, the Early (Q1), Middle (Q2), and Late Pleistocene (Q3), and the Holocene (Q4). Six lithofacies include lacustrine, fluvial, coastal, drowned river channel, deltaic, and shallow marine in these time periods. The fluvial and lacustrine lithofacies prevailed during Q1and Q2; coastal and drowned river channel lithofacies periodically appeared in Q1, Q2, and Q3; shallow marine lithofacies dominated Q3; and deltaic lithofacies occurred in Q4. Based on stratigraphy, four transgressive events are inferred. Trace-element (Sr, Ba, B, Ga, V) content and ratios of Sr/Ba and B/Ga are considered with regard to their distribution in the various lithofacies. Geochemical facies criteria are established based on combined diagnostic indices: Sr > 160 ppm, B > 90 ppm, Sr/Ba > 0.35, B/Ga > 4.0 for the shallow marine lithofacies; Sr < 90 ppm, B < 50 ppm, Sr/Ba < 0.2, B/Ga < 2.5 for the terrigenous lithofacies. These indices correspond well to paleosalinity data obtained using the sedimentary phosphate method (Ca/Ca + Fe). Transgressive events identified by the geochemical indices are mostly the same as reflected by marine fossils. Nevertheless, geochemical indices can indicate the occurrence of a weak transgression, where marine fossils are rare.