A population estimation of proboscis monkeys (Nasalis larvatus) has been conducted in Manggar River, Balikpapan. In this non-conservation area, the anthropogenic activities threaten the proboscis monkey habitat. Boat survey technique was applied along ± 17 km of the river in the morning and evening. The number of proboscis monkeys in the surveyed area was estimated to range from 57 to 69 individuals with estimated population density of 4.75 individuals/Km2. Moreover, the population of this primates was divided into 4 groups and the sex ratio between adult males and females was 1:2.33. The proboscis monkeys were distributed in the middle of the river to the upstream. The highest population was found in the upstream area with less human activities. Conservation efforts in the Manggar River need to be carried out considering the proboscis monkey habitat in the area has been fragmented and isolated. These efforts could involve local economic communities.