Change in water quality was investigated with laboratory-scale ozone-biological activated carbon filters using copper-modified granular activated carbon (Cu/GAC) and unmodified granular activated carbon (GAC). In the first seven days of the experimental period, Cu/GAC removed organic matter more efficiently owing to its enhanced adsorption capacity. As the running time increased, the amount of disinfection by-products (DBPs), dissolved organic carbon, and extracellular polymeric substances (EPS) increased sharply in the effluent of the Cu/GAC filter (CCW). More importantly, the EPS suspended in the CCW exhibited weaker flocculating efficiency and hydrophobicity, causing more active chemical reactions between chlorine and EPS substances. The copper species significantly limited the microbial biomass (0.01 nmol/L adenosine triphosphate) but stimulated the secretion of significant amounts of EPS by microorganisms for self-protection. Furthermore, the microbial community in the bulk water was successfully shaped by Cu/GAC, resulting in a continuous supply of EPS-derived DBP precursors and a sharp rise in chlorine consumption in the downstream drinking water distribution. Therefore, use of modified GAC materials, similar to Cu/GAC, as carrier materials for biological activated carbon (BAC) treatment remains controversial, despite enhanced pollutant adsorption capacity. This is the first study to reveal the mechanism of BAC-modified materials for water quality stability. The study potentially contributes to a comprehensive understanding of the effects of biofilm transformation and microbial community succession on drinking water quality. These results showed that tap water safety risks could be reduced by improving BAC pretreatment in drinking water treatment plants.