Nearly all water supply systems for medium or high -rise buildings in Egypt include storage cisterns to feed the upper floors with cold-water for different uses. Although, these cisterns are the most important component in the distribution system, they are generally the least understood in terms of their effect on water quality. In this study, chlorine residual, algae genus and concentration, and pH value were measured before and after storage cisterns that exist over a 12-floors building in Assiut City to check their effect on water potability, through 48 hours of observation. EPANET quality model is applied to simulate the chlorine residual and water age in the distribution system and storage cisterns through extended period simulations. The applied software implements a Lagrangian time-based approach to track the fate of discrete parcels of water as they move along pipes and mix together at junctions and cisterns. Residual chlorine reaction coefficients for the investigated system that match the field measurements are optimized. The model is used to study the influence of the storage cisterns size and the turnover depth on residual chlorine decay and water age in the tanks. Results indicated that, oversized storage cisterns can have negative impacts on water quality, including increased water age, reduced disinfectant residuals, and increased growth of disinfectant by-products (DBPs). Some of the microbiological and chemical effects of the cisterns on water quality have been investigated. More researches are needed to check DBPs levels in the water leaving such storage cisterns.