Polycyclic musks (PMs), widely used in the cosmetic and perfume industries, are gaining attention as a new type of persistent organic pollutant (POP). The related contamination in developing countries, such as China, where the use of these compounds is increasing, needs to be closely monitored. This work systematically studied the distribution profile (water-suspended particulate-sediment-porewater) of PMs in Haihe River, China. The average concentrations of PMs were comparable to those of the traditional POPs. The typical PMs (galaxolide and tonalide) exhibited different environmental behaviors in various media. Water played a more significant role than suspended particulates in the transport of pollutants. Importantly, this work explored the relationships among PMs, surfactant, phosphorus, carbon, salinity, heavy metals and pesticides. Unlike previous reports focusing on the relationships among PMs, wastewater discharge and population distribution, this work innovatively studied the distribution characteristics of pollutants by principal components analysis. The results suggest that PMs can be used as a chemical marker indicating domestic contamination.