This research analyses the characteristics of pollution sources and evaluates the water quality of the Bedadung River at the Perumdam Tirta Pandalungan water intake, as a component of the municipal waterworks for the Jember Regency. Utilising self-purification optimisation with linear programming and the Indonesian water quality classification, the study unfolds in a systematic fashion. The research was broken down into the following stages: (1) analysis of the characteristics and distribution of pollution sources, (2) capacity determination using mass balance and the Streeter– Phelps method, and (3) optimisation of organic pollution sources. The input data for the study comprised biochemical oxygen demand (BOD), discharge, river profile, and dissolved oxygen (DO). The pollution source identification results around the Bedadung River segment showed that 13 wastewater monitoring points were dominated by domestic activities with quality (BOD) in the range 1.01–3.18 mg∙dm^–3. This did not exceed the established domestic wastewater quality standards in Indonesia. The total pollution load capacity – BOD at the Perumdam Tirta Pandalungan water intake in the Sumbersari (T2) and Kaliwates (T3) segments was determined using self-purification optimisation and it exceeded class I designation standard for river water quality established by the Indonesian government. The maximum BOD value using self-purification optimisation in the Sumbersari (T2) segment was 11.44 mg∙dm^–3 compared to 13.45 mg∙dm^–3 in the Kaliwates (T3) segment. The maximum BOD for class I water quality is 2 mg∙dm^–3. The class I water quality standard is thus more stringent in maintaining river water quality compared to self-purification.