Sources and molecular composition of dissolved organic matter (DOM) in coastal rivers have been tightly linked with its reactivity and fate, thus influencing element and nutrient cycling. The DOM in coastal rivers is usually sourced from both terrestrial and marine inputs, with further complication by anthropogenic activities, which is less understood in coastal rivers located near populated industrial regions. In this study, DOM in a typical anthropogenically influenced coastal river, Daliao River, was analyzed for optical analyses and for molecular composition via Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) to give a better scope of composition and sources of DOM. The DOM was enriched in autochthonous and anthropogenic inputs at upstream sites according to high chlorophyll a concentrations, strong protein-like fluorescence, and nonoxygen heteroatomic CHOS formulae (19–24% by relative peak intensity) detected by FT-ICR MS analysis. A series of surfactant-like formulae, indicative of wastewater inputs, were identified and showed a decreasing trend from upstream to the river mouth. Compared with large world rivers, the DOM of Daliao River is characterized by higher abundances of heteroatomic (excluding O) formulae and molecular lability, which is likely caused by strong autochthonous and anthropogenic inputs. In general, we demonstrate that in addition to optical properties, the molecular composition can assess the specific anthropogenic imprints and molecular lability of DOM, which is essential for constraining sources and identifying processes during the transit of DOM from the river to estuary with increasing urbanization and industrialization.