The Brantas River that crosses several districts and cities in East Java province receives pollutant loads from various human activities along its watershed. On the other hand, the Brantas river is also used as a source of water from various human activities along the watershed. Naturally, the river has the ability to recover through physical, chemical and biological processes. The ability of river to recover from pollution can be seen from the rate of carbon deoxygenation. Therefore, conducted research to see the performance of Brantas river self-purification starting from upstream in the Pendem Batu Bridge to the downstream at Padangan Mojokerto Bridge with 11 (eleven) locations of water sampling. Carbon deoxygenation determination method using Thomas method. The results showed varying deoxygenation rates with a range of values 0.001 / day to 0.028 / day. The highest rate of Carbon deoxygenation lies in the sampling location at Kesamben Bridge Blitar and the lowest is at the location at Dinoyo Bridge Malang. Brantas river deoxygenation rates is lower than Metro river in Malang regency, Brantas river in Malang city, Citarum upstream river, Cikapundung river and Citepus river. So it is concluded that the Brantas river self-purification performance from Carbon deoxygenation rate is lower. Brantas river management efforts should consider this factor in the handling of organic pollutant sources. The wastewater quality standard that have the same value.