Abstract. The Mekong River in Southeast Asia thanks its regular annual flood to the southwest monsoon. At longer time scales, the monsoon is a spatially and temporally variable circulation, with different annual to millennial variation for different regions. In this paper, the Indian and the Western Pacific components of the monsoon were analyzed to draw a light on the interannual flood variability of the Mekong River. The focus is on the variance of flood season flows at 8 stations on the Mekong River, as well as on well-known climate indexes that reflect the dynamics of the monsoon circulation and ocean temperature anomalies. An effort was made to identify the temporal resolution that contains most of the interannual variability of both flood regime of the Mekong and monsoon intensity. We found a close connection between the Western Pacific monsoon and the discharge in Kratie and other stations in the Southern Mekong region. In the frequency domain, the interannual to decadal variance of the Mekong discharge closely follows that of the Western Pacific monsoon. More importantly, the well-known regime shift of 1976 in the North Pacific is detectable in the frequency domain for flood discharge and monsoon intensity. This suggests a relationship between Pacific sea surface temperature and monsoon variance, which is a good predictor for flood variance. This dependence influences the probability of occurrence of floods in the Mekong Delta.