Ciliwung River is one of the rivers crossing West Java and special capital region of (DKI) Jakarta provinces which plays an important role in fulfilling the needs of human activities and living things surrounding it. Designated as a national priority for management, the Ciliwung River that runs from Mount Pangrango (upper stream) to Jakarta Bay (lower stream) has received pollution from results of human activities such as household activities, agriculture, plantations, animal husbandry, industry, and recreation areas. In addition, the decreased green cover in the upstream area also adds more pressure on the quantity of water in the Ciliwung River. The purpose of this study was to determine the trend of water pollution in the Ciliwung River in the period of 2011-2014 based on physical, chemical and biological parameters. Samples were taken from 22 points starting from upstream to downstream area. From 15 water quality parameters, there were only three parameters, namely total dissolved solid (TDS), pH and nitrate (NO3-N) which still meet water quality criteria class II based on Government Regulation number 82/2001, in all observation periods and sampling sites. Other parameters invariably meet or beyond the water quality criteria. Pollution trend increased towards the downstream of Ciliwung River, however annual comparisons across the year of observations did not show significant differences. High pollution in the downstream area was caused by accumulated pollutants coming from waste disposal of densely populated area and diverse activities in the downstream. Fecal coliform bacteria and total coliform contributed the highest pollution in the Ciliwung River compared to other pollutants. Both those two parameters greatly exceed the water quality criteria at all sampling sites, except in the Ciliwung river spring. Controlling those two parameters may improve Ciliwung water quality.