Due to the failure of municipal supply systems in many Nigerian cities, residents often resort to long storage of water in large high-density polyethylene (HDPE) tanks in order to reduce water stress. This paper investigated deterioration of the quality of stored water for a period of 35 days. Samples from 20 purposively selected storage tanks in Enugu, Nigeria were collected for analysis. Heterotrophic bacteria, total coliform (TC), enterococci and Escherichia coli were present in 85%, 75%, 40% and 61% of the samples, respectively. E. coli (p < 0.001) and heterotrophic plate count (HPC) (p < 0.001) were significantly higher in storage tanks that were also used for rainwater collection than those that were not. HPC and TC counts in tanks that collect rainwater were twice those of tanks that do not, while E. coli and enterococci counts in tanks that also collect rainwater were three times those of tanks that do not collect rainwater. The most significant change (p < 0.001) in E. coli concentration occurred after 15 days of storage. Cleaning of tanks caused significant reduction of TC counts (p = 0.013), E. coli (p < 0.001), HPC (p < 0.001) and enterococci (p = 0.001). Hence, prolonged storage of water causes significant deterioration of water quality.