Abstract: Exploring water quality status, water problems and pollution sources in the Qinhuai River catchment is the basis for the improvement and protection of water environment, which is of great significance to constructing ecological civilization. Water quality parameters at 29 sites were investigated from January 2015 to December 2019 in the Qinhuai River catchment, Nanjing, China. The Nemeiro pollution index method and positive matrix factorization (PMF) were used to determine the water quality status and pollution sources. The results showed that nitrogen pollution and organic pollution were the most important types of pollution in the Qinhuai River Basin, of which TN pollution was the most deteriorated one. A improving trend of water quality was observed at the interannual scale, while the water quality in the non-flood season was worse than that in the flood season on the seasonal scale. Water quality parameters displayed different spatial distribution patterns during flood season and non-flood season, and the high-polluted areas were mainly concentrated in the lower reaches of the Qinhuai River and Jiangnang University Town. The results of PMF indicated that the contribution rates of pollution sources displayed different temporal distribution patterns during flood season and non-flood season. Domestic sewage and business service sewage, non-point source pollution, industrial wastewater contributed largely pollution to the whole watershed. Non-point source contributed more Nitrogen and Phosphorus to the watershed in flood season than that in non-flood season, while industrial wastewater contributed more nutrient to the watershed in non-flood season than that in flood season. Therefore, relevant departments should consider the seasonal differences and characteristics of regional pollution when formulating water environmental protection and governance countermeasures.The research results can provide a scientific basis and foundation for the water environment management and control in the Qinhuai River Basin.