The Mekong River Basin (MRB) is one of the significant river basins in the world. For political and economic reasons, it has remained mostly in its natural condition. However, with population increases and rapid industrial growth in the Mekong region, the river has recently become a hotbed of hydropower development projects. This study evaluated these changing hydrological conditions, primarily driven by climate as well as land use and land cover change between 1992 and 2015 and into the future. A 3% increase in croplands and a 1–2% decrease in grasslands, shrublands, and forests was evident in the basin. Similarly, an increase in temperature of 1–6 °C and in precipitation of 15% was projected for 2015–2099. These natural and climate-induced changes were incorporated into two hydrological models to evaluate impacts on water budget components, particularly streamflow. Wet season flows increased by up to 10%; no significant change in dry season flows under natural conditions was evident. Anomaly in streamflows due to climate change was present in the Chiang Saen and Luang Prabang, and the remaining flow stations showed up to a 5% increase. A coefficient of variation <1 suggested no major difference in flows between the pre- and post-development of hydropower projects. The results suggested an increasing trend in streamflow without the effect of dams, while the inclusion of a few major dams resulted in decreased river streamflow of 6% to 15% possibly due to irrigation diversions and climate change. However, these estimates fall within the range of uncertainties in natural climate variability and hydrological parameter estimations. This study offers insights into the relationship between biophysical and anthropogenic factors and highlights that management of the Mekong River is critical to optimally manage increased wet season flows and decreased dry season flows and handle irrigation diversions to meet the demand for food and energy production.Published version