Glycerol dialkyl glycerol tetraether (GDGT)-based proxies are increasingly used in modern carbon cycling and palaeoenvironmental investigations. It is therefore crucial to examine the robustness (sources, transport and degradation) of all GDGT-based proxies in continental margins, where sedimentation rates and extent of carbon cycling are high. We have analyzed the distributions of GDGTs in surface sediments from the Lower Yangtze River and East China Sea (ECS) shelf. The results revealed multiple sources and complex shelf processes that govern the distributions. The isoprenoid GDGT-inferred sea surface temperatures (SSTs) are robust and reflect the satellite-derived annual mean SSTs on the shallow ECS shelf, confirming an origin from surface water column-dwelling crenarchaeota. The input from methanogen-sourced, isoprenoid GDGTs is significant in the river surface sediments but they are almost absent from the ECS shelf. Branched GDGTs are also abundant in the river sediments, but ca. 95% are degraded in the Yangtze estuary, a much greater extent than observed for other terrigenous organic matter (OM) proxies. There is also evidence for production of branched GDGTs in the oxic ECS shelf water column and the anoxic sediments/waters of the Lower Yangtze River. As a result, branched GDGT-based proxies in the lower river and ECS surface sediments do not reflect the catchment environmental conditions. The effective degradation in the estuary and widespread aquatic contributions of branched GDGTs improves our understanding of how to use branched GDGT-based proxies in marginal seas.