This study developed a new method to determine the residues of 13 organophosphorus flame retardants (OPFRs) in drinking water by gas chromatography-tandem mass spectrometry (GC-MS/MS) technique and investigated the chemical distribution in water samples from municipal plants along the Yangtze River in Nanjing. The linear calibration correlation coefficients R2 for all 13 OPFRs were at least 0.998 0. Three levels of spiked test were performed. Most of the recoveries were in the range of 80~120%, and the relative standard deviations (RSDs) for the 13 OPFRs were 2.1~17% (n = 6). Five OPFRs were 100% positively detected in the samples, and 3 OPFRs were positively detected in some samples. The concentrations of detected OPFR in the water ranged from 0.7 to 5780.0 ng L-1. The average concentrations of OPFRs in wet season were higher than those in dry season, and the contaminants mainly originated from the source water in the Yangtze River. The exposure assessments of individual and total OPFRs were investigated. The estimated daily intakes of total OPFRs via ingestion of drinking water reached up to 64.8 and 45.2 ng/kg bw/day in dry and wet season, respectively. This study demonstrates a profile of OPFR distribution in Nanjing municipal water and provides information on human exposure assessment via drinking water in the Nanjing District, China.