We used a suite of two models: a global climate model, and a hydrological routing scheme, to estimate the changes in the surface water budget and extent of natural wetlands, at the last interglacial (126000 years ago) and at the last glacial maximum (21000 years ago). At both time periods, in northern tropical Africa as well as in northern South America, our simulations exhibit, in many places, an indirect relationship between the surface water budget and the extent of natural wetlands. In relatively moist regions, decreasing (increasing) rainfall and runoff at the glacial maximum (last interglacial) result in increased (decreased) wetland area due to the reduction (increase) in lake depth. This counter-intuitive result has never been hypothesized before and may shed a new light on the interpretation of past changes in atmospheric methane, as derived from ice core analyses. It also points to the importance of using a bottom-up modelling approach in this field of study.