We used Global NEWS to analyze the effects of dams in large rivers on nitrogen (N) and phosphorus (P) inputs to the coastal waters of Indonesia for the period 1970–2050. We model N and P export by rivers, taking into account nutrient retention on land, during river transport and in dammed reservoirs. Our results indicate that N and P export by rivers to coastal seas may increase over time. In the past the N and P inputs to coastal waters of Indonesia were low and have increased relatively fast since 1970 as a result of human activities. For the coming decades we calculate that P inputs to coastal waters in Indonesia may double while N inputs may increase by up to 20%. Damming may slow down these increases to some extent. Our study illustrates that it is important in river nutrient export models to appropriately account for nutrient retention in dam waters.