Commercial chemicals, such as synthetic musks, are of global concern, but data on their occurrence and spatial distribution in aquatic environments of large scale are scarce. Two sampling campaigns were conducted in the present study to measure freely dissolved synthetic musks in freshwaters across China using passive samplers, along with biological coexposure at selected sites. Polycyclic musks (PCMs) dominated synthetic musks, with a detection frequency of 95%. Higher concentrations of PCMs were observed in densely populated Mid, East, and South China compared to less populated regions, indicating the significance of anthropogenic activities for synthetic musks in water. The concentration ratios of galaxolide (HHCB)/tonalide (AHTN) were significantly higher in low-latitude areas than in high-latitude areas from June to September, suggesting that solar radiation played an important role in the degradation of HHCB/AHTN. Significant correlations were found between dissolved concentrations of HHCB and AHTN and their lipid-normalized concentrations in coexposed fish and clam. The estimated hazard quotients for HHCB and AHTN in freshwater fish consumed by humans were less than 0.01 at all sampling sites except the Yangtze River Basin. These results help to understand the environmental fate and ecological risks of synthetic musks on a large geographical scale.