Jakarta, located on a coastal alluvial plain in Indonesia, is one of the Asian megacities. According to previous studies, it is estimated that the load of biochemical oxygen demand (BOD) from lands to sea is so large in Indonesia. Therefore, it is necessary to conserve river and marine water environments by confirming pollution characteristics of rivers in megacities such as Jakarta. However, species, seasonal and spatial variation, and sources etc. of pollutants have not been clarified. In this study, we aimed to confirm the present status and seasonal and spatial variations of pollutants and to estimate pollution sources and attenuation in Ciliwung River which flows from volcanic mountains to Jakarta bay via central Jakarta. River water samples were collected at 20 sites located in mid to downstream in June and August of dry season and in April and December of rainy season in 2010 with collecting some sewage samples. Water samples were analyzed for BOD, dissolved organic carbon, major anions and nutrients. BOD, DOC and NH4-N concentrations in Ciliwung river were very high, and average and the highest values were 14.8 mg/L and 70.0 mg/L, 11.1 mg/L and 41.7 mg/L, and 2.6 mg/L and 15.4 mg/L, respectively. BOD values extremely exceeded the environmental standard of Japan. In addition, a very large seasonal variation was observed in only BOD. They were from 3.5 mg/L in average of December to 26.1 mg/L in June. These results suggest that organic pollutants accumulated on riverbed during dry season were flushed out at a beginning of rainy season and organic decomposition occurred significantly in a rainy season due to increase of oxygen supply. Since flushing of pollutants at a beginning of rainy season would affect to coastal environments, it is necessary to estimate them. In spatially, BOD concentrations declined significantly with flowing down even though sewage is supplied at many places without treatment. Especially, spatial variations in ratios of BOD and Clalso suggest natural attenuation with high activity in a river under the high temperature. *1 広島大学大学院総合科学研究科 Graduate school of Integrated Arts and Sciences, Hiroshima University (現:復建調査設計株式会社 Fukken Co. Ltd.) *2 広島大学大学院総合科学研究科 Graduate school of Integrated Arts and Sciences, Hiroshima University *3 LIPI(インドネシア科学院) R&D center for geotechnology-LIPI *4 日本学術振興会特別研究員PD,愛媛大学沿岸環境科学研究センター JSPS PD, Center for marine environmental studies, Ehime University(現:岡山大学大学院環境生命科学研究科 Graduate School of Environmental and Life Science, Okayama University) *5 広島大学大学院総合科学研究科 Graduate school of Integrated Arts and Sciences, Hiroshima University (現:日本学術振興会特別研究員PD,(独)農研機構 近畿中国四国農業研究センター JSPS PD, National agriculture and food research organization western region)