China prioritizes ensuring drinking water safety, particularly in the water-scarce northwest region. This study, utilizing water quality data from 52 village and town water sources since August 2022, assesses water quality, with a specific focus on key indicators related to organic pollution sources. This study provides a scientific foundation for enhancing water quality in these sources. Employing category factor analysis for classification and grading, principal component analysis for qualitative analysis of key evaluation indicators, and the absolute principal component linear regression equation for quantitative calculation of pollution sources, this study reveals that all 52 water sources meet quality standards. Principal component analysis categorizes pollution sources as diverse types of organic compounds in surface water. Source analysis calculations highlight decay-type organic substances as major contributors to increased water color and permanganate index, with pollution contribution rates of 54.78% and 31.31%, respectively. Fecal-type organic substances dominate the increase in dissolved total solids and total coliforms, with pollution contribution rates of 56.65% and 40.16%, respectively. Additionally, high-molecular-weight organic substances exhibit lower concentrations in the water. This article presents a systematic water quality assessment methodology, which is used for the first time to qualitatively assess the types of water sources and to quantitatively trace specific sources of organic pollution in source water in northwest China. This systematic study’s results, involving initial assessment followed by traceability, recommend the adoption of a simple contact filtration and disinfection process to enhance water quality in the region.