The chemical composition of dissolved organic matter (DOM) exerts significant influence on aquatic energy dynamics, pollutant transportation, and carbon storage, thereby playing pivotal roles in the local water quality and regional-global biogeochemical cycling. However, the effects of natural climate change and local human activities on watershed characteristics and in-river processes have led to uncertainties regarding their contributions to DOM chemistry in coastal rivers, creating challenges for effective water management and the study of organic matter cycling. In this investigation, we employed a combination of stable isotopic analysis, optical techniques, and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) to elucidate the sources, optical properties, and molecular composition of DOM in three South China coastal rivers. Our results suggest that terrestrial DOM entering the three rivers through natural or anthropogenic pathways is gradually diluted by in situ primary production as it moves downstream, ultimately being influenced by seawater intrusion near the estuary. Additionally, terrestrial processes influenced by temperature likely govern DOC concentration, while seawater intrusion promotes the natural production of S-containing organic compounds. In contrast, human-altered landcover significantly impacts DOM molecular composition. Increased water areas lead to the enrichment of lignins with high disinfection byproduct formation potential, and agricultural residue burning appears to be the dominant source of pyrogenic DOM in these coastal rivers. Our distinct results suggest that the development of specific water management plans that consider the combined effects of temperature, seawater intrusion, landcover changes, and agricultural practices will be essential to ensure sustainable water resource.