Although many households in the Kathmandu Valley rely on household water treatment and safe storage (HWTS) to obtain drinking water, the safety of treated water has not been evaluated in actual usage. Therefore, we assessed the performance and maintenance of five HWTS methods used in 101 households. The choice of HWTS methods by households was primarily influenced by the raw water source, that is, jarred water users opted for boiling and groundwater users selected reverse osmosis with ultraviolet irradiation (RO-UV). While boiling and electric dispensers (ED) did not remove inorganic contaminants (ammonia nitrogen, arsenic, and manganese), ceramic candle filters (CCF) and RO-UV reduced them moderately. The HWTS methods reduced E. coli and total coliforms (TC) by 95.8 and 84.1%, respectively, but 11.8 and 69.3% of treated water samples remained positive for these two bacteria. Combined methods (CM) and RO-UV showed an inferior TC reduction compared to the simpler HWTS methods, boiling, CCF, and ED, possibly due to difficulties with regular maintenance and storage contamination. Therefore, it is recommended to choose simpler HWTS methods that meet the requirements of the household’s water sources rather than more expensive and difficult-to-maintain methods, which should be chosen only if the raw water contains high concentrations of inorganic contaminants.