Dissolved organic matter collected in Daning River (China) in July 2009 was investigated with parallel factor analysis (PARAFAC) and fluorescence spectroscopy with the aim of identifying the origin of dissolved humic substance (HS) components. Two HS-like fluorescence components (peak M and C) with excitation/emission (ex/em) maxima at 305/406 nm and 360/464 nm showed relatively uniform distribution in the vertical direction for each sampling site but a trend of accumulation down the river, independent of the highly heterogeneous water environment as implicated by water quality parameters (i.e., water temperature, algae density, chlorophyll a, dissolved oxygen, dissolved organic carbon, pH, conductivity and turbidity), while an amino acid/protein-like component (peak T; ex/em = 280/334 nm) was quite variable in its spatial distribution, implying strong influence from point sources (e.g. sewage discharge) and local microbial activities. The fluorescence intensity (Fmax in Raman units) at these ex/em wavelength pairs fell in the range of 0.031–0.358, 0.051–0.224 and 0.026–0.115 for peak T, M and C, respectively. In addition, the Fmax values of peak C covaried with M (i.e. C = 0.503 × M, p < 0.01, R2 = 0.973). Taken together, these results indicate that peak M and C originated primarily and directly from the same soil sources that were diffusive in the catchment, but peak T was more influenced by local point sources (e.g. wastewater discharge) and in situ microbial activities. This study presents new insights into the currently controversial origin of some HS components (e.g. “peak M”, as commonly referred to in the literature). This study highlights that natural water samples should be collected at various depths in addition to along a river/stream flow path so as to better evaluate the origin of HS fluorescence components.