Rapid population growth, urbanization, and changing weather patterns have significantly impacted water quality and quantity in the peri-urban region of Nepal, leading to water scarcity. This study assessed the Water Quality Index (WQI) of six different water sources in the Thaha Municipality, Makwanpur district, during the monsoon (September 2022) and winter (January 2023) seasons. The water sources evaluated included spring water distributed by a pipe (SP1, SP2, SP3, and SP4), bore-well water distributed by a pipe (BP), and a well (W). The mean values of electrical conductivity, pH, total alkalinity, total hardness, calcium hardness, chloride, biological oxygen demand, nitrate, and arsenic, were within the World Health Organization (WHO) and National Drinking Water Quality Standards (NDWQS) limits. However, the mean values of turbidity, iron, ammonia, and phosphate exceeded the standard limits of the WHO and NDWQS. E. coli was detected in all six sources during the winter season and in four sources (SP1, SP2, BP, and SP4) in the monsoon season. In the monsoon season, the WQI for SP1 (4.23) and BP (4.78) was in the excellent category, while SP3 (29.27) was good. In the winter season, the WQI for SP1 (84.57) and SP3 (78.68) was very poor, and SP4 (43.94) was poor. SP2 (44.11) and SP4 (43.94) were good, while W was unsuitable for drinking (>100) in both seasons. The poor water quality of some sources could be attributed to various anthropogenic activities around water sources. Fluctuating WQI underscores the need for continuous oversight and interventions to ensure safe drinking water for peri-urban areas.