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To investigate the change in water quality from the source to the point-of-consumption (PoC), we collected and analyzed 56 water samples from various points of an intermittent water supply system in the Kathmandu Valley, Nepal. Compared to treated water from treatment plants, distribution network samples showed large spatial and temporal variations in total dissolved solids (TDS), Fe, Mn, NH4-N, coliforms, and free and total chlorine concentrations due to irregular supplies, intrusion of contaminants, and uneven dosing of disinfection chemicals. Water quality in the household storage tanks was poorer than that in the distribution network for TDS, NH4-N, E. coli and total coliforms, suggesting contamination in the storage tanks. There were no significant differences in water quality in the rooftop and the basement tanks, yet the median TDS, Mn, and E. coli concentrations in the rooftop tanks were higher than in the basement tanks possibly because of its exposure to the environment and low frequency of cleaning. The age of the basement tank and the source of water (piped or tanker-delivered) had no effect on the microbial quality of the stored water, whereas higher cleaning frequency significantly reduced E. coli concentrations. Household water treatment systems were effective in reducing NH4-N, Mn, Fe, TDS, and E. coli concentrations, but total coliform concentrations increased at the PoC possibly due to microbial regrowth or improper storing and cleaning practices. Guidelines for maintaining residual chlorine levels in the basement tank and redesigning rooftop tank to ease cleaning are suggested as potential measures to improve water quality during storage.