China is undergoing unprecedented rapid urbanization, which is accompanied by the formation of more than 2000 black and odorous urban rivers. Dissolved organic matter (DOM) is an essential component in aquatic ecosystems and regulates the carbon and nutrient cycle, but its characteristics in highly polluted urban rivers are still not well understood. Here, water samples from the mainstream, tributaries, ponds, and reservoirs within the highly urbanized Maozhou River watershed (Shenzhen, China) were analyzed using absorption and fluorescence spectroscopy, stable carbon isotope analysis, and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) to explore the impact of urbanization on DOM characteristics. The results showed elevated dissolved organic carbon concentrations in the disturbed waters (mainstream, tributary, and pond) compared to those in the reservoir water. Results of the spectroscopic, isotopic, and FT-ICR MS analyses suggest that disturbed water DOM had lower aromaticity, average molecular weight, and plant-and soil-derived terrestrial (e.g., lignin-like) contributions but greater contributions from microbial-derived protein-like and anthropogenic sulfur-containing compounds (e.g., synthetic surfactants) than those of reservoir DOM. These characteristics were strengthened from the upper to the lower mainstream, which implies greater anthropogenic impact on downstream waters. Point-source wastewater effluent input caused increases in DOM level in the mainstream water and abrupt changes in DOM characteristics with very strong anthropogenic characteristics. The distinct chemistry of urban DOM from natural organic matter highlights a potentially strong impact of rapid urbanization on carbon and nutrient cycle in aquatic ecosystems.