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The Citarum River in West Java is the largest water supplier to the Saguling Dam, which plays a major role in electric power generation for the entire Java Island and is used for the aquaculture of marketed fish. To elucidate the extent of degradation in water quality and its causes in the Upper Citarum watershed, physical, chemical and biological parameters for water samples collected from various sites were analyzed. The results demonstrate large site-to-site variations in water qualities and pollutant loads derived from various human activities such as agriculture, cattle raising and the textile industry. To halt worsening conditions of the Citarum watershed, integrated mitigation efforts should be made, taking biophysical pollution mechanisms and local socioeconomic conditions into account.