In Ciliwung River, pollutant sources coming from domestic waste, breeding, and industry with total waste load of about 212 ton BOD/day and estimated in the year 2020 will reach 280 ton BOD/day. Whereas, discharge in Katulampa weir of 10.24 m3/s and 195 m3/s as minimum and maximum discharge respectively, indicate that Ciliwung water quality is very heavily polluted especially in the dry season after passing Bogor Municipality until Jakarta Bay. The water quality modeling applied a finite segment method calibrated with spatial variation at one time by using real time sampling water quality data in order to obtain accurate results of model calibration. Recovery strategies for the existing very heavily polluted water quality shall apply a water quality target program that has to be completed by the end of the year 2020. Study results recommend a recovery applying a short-term program up to the year 2012 as preparation stage for restructuring water quality and reviewing the waste load permit. Whereas, the mid-term program shall put into effect the waste water permit for domestic and industry activities, and wastewater treatment plant performance auditing. The long-term program shall concentrate on hazardous waste disposal and application of clean industrial technology.