Mun River is the largest tributary of the Mekong River in Thailand and provides abundant water resources not only for an important agricultural area in Thailand but also for the lower Mekong River. To understand how the runoff of Mun River responds to climate change and human activities in recent decades, this study performed a detailed examination of the characteristics of runoff variation based on measurements at two hydrological gauging stations on the main stem of Mun River during 1980–2018. Using the Mann-Kendall test, Morlet wavelet transform and Double Cumulative Curve methods, this study identifies that the variation of annual runoff of Mun River encountered an abruption in 1999/2000, with an increased trend taking place since then. Furthermore, a detailed assessment of the effects of the variations in rainfall, temperature, evaporation, and land use types extracted from remote sensing images at the basin scale reveals that a significant reduction in forest area and slight reductions in evaporation and farmland area taking place since 1999 can lead to an increase in the runoff of Mun River, while the dramatic increase in garden area since 1999 tends to make the runoff decrease.