This article analyzes past and future trends in nutrient export of dissolved and particulate nitrogen and phosphorus by rivers into the coastal waters of Indonesia. The focus is on 19 rivers included in the Global Nutrients Export from WaterSheds model. In the past, export of dissolved inorganic nitrogen by rivers doubled, while export of other forms of nitrogen and phosphorus by rivers did not change largely. For future trends of four Millennium Ecosystem Assessment scenarios, the largest increases are calculated for river export of dissolved inorganic phosphorus by rivers caused by increased inputs from sewage systems. The export of other nutrient forms is relatively constant in time, which is surprising, given the growing population and the associated increasing inputs of nitrogen and phosphorus to the land. Changes in export by rivers are the net effect of human activities and changes in hydrology. The results indicate that future increases in nitrogen and phosphorus inputs on land are partly counterbalanced by decreases in basin discharge as a result of climate change and consumptive water use. These results differ from other Asian regions, for which large increases in nitrogen and phosphorus inputs to coastal waters are calculated. This can be explained by population growth, gross domestic product increase, and sewage system development.