The Pearl River drains the second largest watershed in China, funnelling large amounts of freshwater and organic matter into the northern part of the South China Sea through an estuary characterized by pronounced biogeochemical gradients. In this study we analyzed organic extracts of surface sediments collected along land-sea transect that captures a transition from freshwater environment at the site of the Pearl River discharge, to marine settings at the most distal sampling point in the coastal South China Sea. Samples were analyzed using Fourier transform ion cyclotron mass spectrometry (FTICR-MS), to assess the molecular composition of the organic species present in the sediment and understand the sources and diagenesis of deposited organic matter. Results show a complex mixture of molecular markers, many of which can be used as proxies to distinguish between the freshwater and saline settings. For example, geochemical signal at the freshwater site is notably characterized by species belonging to hydrocarbon and sulphur-containing compound classes – these are likely markers of terrestrial, natural and/or anthropogenic organic matter inputs. On the other hand, samples from the coastal marine site bear a unique signature of putative tetrapyrrole species, molecular indicators of phytoplankton phaeopigments. Notably, some unusual and or novel species, such as sterenes and alkanones were putatively identified. These and other biomarkers species that can be detect using our single injection method provide convenient multiple proxies necessary for interpreting dynamic changes from land to the ocean, which have even been complicated by anthropogenic activities.