Self-purification plays an important role in water regulating ecosystem services aimed at protecting river water quality from pollutant inputs. The Citarum River is the longest river in West Java, Indonesia where the water quality has declined due to pollutant inputs from domestic and non-domestic activities. This study aims to investigate the status of self-purification ecosystem services and the influence of water quality in the upstream of the Citarum River, in the Cihawuk and Majalaya segments, which are rural and urban areas. The self-purification status was determined by the deoxygenation rate using Thomas’s slope method, and by the reaeration rate according to O’Connor and Dobbins’ method. The polynomial component regression (PCR) was performed to determine the significance of the influence of physicochemical factors on self-purification. The deoxygenation rates (k1) in the rural and urban areas upstream of the Citarum River were 0.044 per day and 0.058 per day, respectively, while the reaeration rates (k2) in the rural and urban areas were 0.196 per day and 0.156 per day, respectively. These deoxygenation and reaeration rates indicate that the self-purification status upstream of the Citarum River has been disturbed. This result also indicates that chemical factors have a significant influence on the deoxygenation process, while the reaeration process is most significantly influenced by physical factors. The deterioration of self-purification in the Citarum River poses a risk to the long-term availability of water resources. Therefore, this research encourages the reduction in the input of organic pollutants and develops a strategic plan for river management.