The Houjing River has long been an environmental victim of economic development. Industries that have settled along the bank of this river may have largely contributed to severe organic wastes pollution. This study collected water and sediment samples at various points along the river and measured concentrations of 61 volatile organic compounds (VOCs) and 128 semi-volatile organic compounds (SVOCs) for a period of 16 months (Feb 2014–June 2015). Our analyses show that elevated levels of VOCs were observed near two industrial areas, Dashe and Renwu industrial parks. High SVOC concentrations were found in the vicinities of the Nanzih Export Processing Zone (NEPZ) and CingPu station, possibly due to considerable effluent discharges of adjacent industrial and residential areas. Comparing this study's findings with the standard values of different governmental agencies and studies similar to this one, the ecosystem of the Houjing River was seriously contaminated. This study could be used by the government as a basis for future and urgent pollution prevention actions aimed at protecting this ecosystem and reducing the negative impacts of these contaminants on the health and well-being of the local residents and the environment.