Water quality evaluation is a crucial component in assessing, analyzing, and mitigating water pollution, playing a significant role in ensuring water environment quality and residents’ water safety. To ensure the safety of centralized surface drinking water sources in Yan’an City, this study monitored water bodies in 10 Class I source water protection areas during March, May, July, August, and October 2019. Based on 63 monitoring indicators, the water quality condition and eutrophication level were assessed using the single-factor evaluation method, the Canadian Council of Ministers of the Environment Water Quality Index (CCME-WQI), and the trophic level index (TLI). Additionally, factor analysis was applied to analyze the main impact indicators and pollution sources. Results indicated significant spatial heterogeneity in water quality across the study area’s source water protection areas, with the exception of the Zhongshanchuan Reservoir, which showed poor in the east and excellent in the west water quality patterns. The single-factor evaluation revealed 11 indicators exceeding the standard, with only 3 water sources meeting the Class II environmental quality standard for surface water, and the rest classified as Class III. WQI evaluation indices ranged from 62.59 to 93.74, with 5 sources having good, 4 medium, and 1 poor water quality. The trophic level index of reservoir-type water sources was 34.41~49.05, indicating a medium nutrient level. The main sources of pollution were agricultural non-point source pollution, oil industry pollution, and domestic pollution. Key indicators affecting water quality were ammonia nitrogen, total phosphorus, total nitrogen, chemical oxygen demand, and five-day biochemical oxygen demand. This study provides a scientific basis for developing pollution prevention measures and management strategies for centralized drinking water sources in Yan’an City.