In this study, samples were taken from three locations, upstream to downstream, along the central route project of the China South to North Water Diversion (SNWD) scheme in summer and winter. These were used to reveal the variations of dissolved organic matter (DOM) during the water transfer process, and the effects of these variations on drinking water treatment and disinfection by-products formation potential (DBPs-FP). The results showed that polysaccharides accumulate in summer and reduce in winter with flow distance, which has an important effect on the overall properties of DOM, as well as on the performance of coagulation, ultrafiltration, and the formation of DBPs. Humic substances, and their hydrophilic content, also increased in summer and decreased in winter with flow distance. In contrast, the concentration of small organic substances (MW ⩽ 1000 Da) increased in both summer and winter with flow distance, which affected both nanofiltration (NF) membrane fouling and DBPs-FP. The results provide a useful case study of spatial and temporal changes in raw water DOM during long distance water transfer and their impact on the treatment and quality of drinking water from the SNWD.