Drinking water supply systems in developing countries operate at irregular intervals and several failures occur more frequently than those in developed countries. Waterborne diseases and microbial contamination of water at tap stands have been related with intermittent supply of water. To understand the spatial and temporal dynamics of faecal contamination and the risk factors associated with intermittent supply, a comprehensive microbial water quality monitoring was conducted in intermittent piped water systems (iPWS) located in remote rural areas of Mid-Western Nepal. Three iPWS’s fed by improved spring water were chosen for the study and monitored daily for a duration of 35 days. Daily water samples were collected from springs, reservoirs and selected tap stands and measured for the concentration of E.coli, total coliforms, pH, turbidity, total dissolved solid and electrical conductivity. Risk factors of contamination were identified by conducting sanitary inspections at sampling points of the supply systems and simple salt tracer tests were conducted to assess the possibility of infiltration into springs. In addition, environmental factors that might influence the microbial quality of water like temperature, precipitation and humidity were monitored daily using sensors and portable devices. The result of the daily monitoring showed that 97.1% of samples collected from spring of iPWS II had detectable E. coli concentration. Similarly, 97.2% of samples from reservoir contained E. coli bacteria above the standard of 0 CFU/100 mL. Moreover, the percentage of contaminated samples at taps went beyond 98%. At iPWS III, 94% of samples collected from spring were contaminated with E. coli while 63% and 73% represents percentage of samples contaminated at reservoir and taps respectively. A higher percentage (92.4%) of water samples collected from iPWS IV were found to be contaminated with E. coli. Water samples tested at sampling points of iPWS IV showed that all samples (100%) from spring, reservoir and distribution chamber were positive for total coliforms. At taps 91% and 99.6% of water samples were found to be contaminated with E. coli and total coliforms respectively. The result of the temporal variability showed peak E. coli concentrations originating from the spring source. Also, the salt tracer test identified infiltration of contaminants from the external environment as a risk factor for contamination. The sanitary inspection result showed that 96.3% of sampling points had medium to very high risk level of contamination. At all iPWS the springs had medium to very high risk level for contamination. Infiltration of contaminants into spring and poor sanitary condition of the supply system affected the microbial quality of water in the study area.