Rapid industrialization, urbanization, and population growth have led to the common occurrence of black-stinking urban rivers. Assessing regional anthropogenic influences is beneficial to develop effective remediation strategies. This study comprehensively investigated the occurrence and fate of linear alkylbenzenes (LABs) as molecular markers of anthropogenic influences in three media (filtered water, suspended particulate matter (SPM), and sediment) in a highly urbanized river (Baihaimian River) in Guangzhou, South China. The concentrations of LABs ranged from 41 to 215 ng/L in the dissolved phase, from 7122 to 46,640 ng/g dry weight in the SPM phase, and from 73 to 3650 ng/g dry weight in surface sediments (0–10 cm depth). The spatial distribution of LABs was probably affected by the surrounding environment, river flux, and sediment properties. No biotransformation of LABs in water samples and a slight biotransformation in sediments were observed. Significant correlations were found between total nitrogen, ammonia nitrogen, and LABs in river water, indicating the same domestic wastewater sources. The positive correlation between total organic carbon (TOC) and LABs in sediments suggested that TOC worked as the controlling factor for the redistribution of LABs and that local sewage discharge was the dominant TOC input. The total mass inventory of LABs in sediment in Baihaimian River was 21 kg. The total mass of LABs released into Baihaimian River was 183 kg per year, among them, 63% was discharged into the adjacent Liuxi River.