Floodplain forests, namely the Várzea and Igapó, cover an area of more than 97 000 km2. A key factor for their function and diversity is annual flooding. Increasing air temperature and higher precipitation variability caused by climate change are expected to shift the flooding regime during this century, and thereby impact floodplain ecosystems, their biodiversity and riverine ecosystem services. To assess the effects of climate change on the flooding regime, we use the Dynamic Global Vegetation and Hydrology Model LPJmL, enhanced by a scheme that realistically simulates monthly flooded area. Simulation results of discharge and inundation under contemporary conditions compare well against site-level measurements and observations. The changes of calculated inundation duration and area under climate change projections from 24 IPCC AR4 climate models differ regionally towards the end of the 21st century. In all, 70% of the 24 climate projections agree on an increase of flooded area in about one third of the basin. Inundation duration increases dramatically by on average three months in western and around one month in eastern Amazonia. The time of high- and low-water peak shifts by up to three months. Additionally, we find a decrease in the number of extremely dry years and in the probability of the occurrence of three consecutive extremely dry years. The total number of extremely wet years does not change drastically but the probability of three consecutive extremely wet years decreases by up to 30% in the east and increases by up to 25% in the west. These changes implicate significant shifts in regional vegetation and climate, and will dramatically alter carbon and water cycles.