The Indochinese section of the Mekong Basin has been subjected to major environmental disturbances over the last half century. The Vietnam War is invoked as a central explanation for the extensive deforestation in specific areas while conflict-induced exoduses caused the abandonment of cultivated lands, followed by forest regeneration. Although the socio-economical consequences of these episodes have been analysed, their hydrological impacts remain unknown. This paper investigates hydrological changes in two catchments of the lower Mekong Basin that were either heavily bombed (in southern Laos) or depopulated (in northern Laos). This analysis is based on the widely and independently recognized fact that vegetation, via evapotranspiration, is a central driver of basin water yield. The analysis of the most complete Vietnam War air mission database and of available hydro-meteorological data over the period 1960–2004 reveals a sharp runoff increase in the southern catchment when bombing climaxed in the early 1970s while no hydrological change is observed in the northern catchment over the same period. From 1995 onwards, the northern and southern catchment's runoff productions are significantly lower and higher than in the pre-war conditions, respectively. Although causalities could not be ascertained because of data limitations, these short- and long-term hydrological shifts were found to be consistent, in terms of occurrence, spatial distribution and magnitude, with the expected changes in the vegetation cover, either denser in the north (in response to abandonment of cultivated lands) or sparser in the south (as a result of bomb-induced deforestation and soil degradations).