This study projects the river discharge in the Magdalena River basin, Colombia, considering projected climate conditions for the 21st century, by using a 20-km-mesh atmospheric global climate model and a 0.5°-mesh global river routing model under a greenhouse gas emission scenario. The climatological annual mean river discharges along the main stream of the Magdalena River do not change significantly, however precipitation, evaporation, and total runoff into the river show statistically significantly changes over most of the Magdalena River basin. By the end of the 21st century, the projected climatological monthly mean river discharge at Puerto Berrio decreases statistically significantly in April, October, and November (P < 0.05), compared to current values, whereas it shows a distinct increase for June through August, thereby reducing the present bimodality of its seasonal variation. Minimum climatological monthly mean river discharge in February could be lower at the end of the 21st century than in the current condition. These results should help increase the awareness of the changing river discharge in the Magdalena River basin, and prepare adaptation strategies to face these challenges.