As a kind of high-organic-content contamination source, extracellular polymeric substances (EPS) secreted by cyanobacteria have become an important factor restricting the safety of supply water. In the dynamic batch mode water supply system, cyanobacterial EPS accelerated the decay rate of residual chlorine, resulting in a 21–26 times increase of the total viable bacteria count within 72 h. The water turbidity exceeded upper limit of the standards for drinking water quality within 4 h, with an increase of 306–332% within 72 h. The biological stability was reduced with BDOC and AOC increased by 41.4–43.8% and 331–396%, respectively. The main cause is that cyanobacterial EPS act as nutrients and metabolic energy for microorganisms, promoting their metabolic activity and secretion of extracellular organic components. This leads to the metabolic accumulation of tryptophan, fulvic acids and humic acids in the pipeline, thus further promoting the regeneration of bacteria. Compared with the influence of biofilm on pipe wall caused by long-term use of water supply network, the contribution of cyanobacterial EPS to the water contamination of pipe network is increased several times. Therefore, even in the presence of residual chlorine, the secondary contamination caused by cyanobacterial EPS in the water supply system could not be neglected.