Abstract Large floodplains are complex ecosystems at the land–water boundary. Because of rainy and dry seasons, most tropical floodplains are subjected to annual water-level fluctuations. During typical low-water periods, extensive areas of the floodplains are dry. However, relatively small geomorphological differences within the boundaries of the floodplains result in comparatively large differences in the length and depth of inundation and, in turn, the establishment of distinct plant communities, called macrohabitats. The specific ecological conditions of these macrohabitats have to be taken into consideration in the development of sustainable management methods and protection measures. Extreme floods and droughts have very strong effects on flora and fauna. The low hydrological buffer capacity of floodplains makes them vulnerable to anthropogenic changes in hydrology and to the impacts of global climate change. This study presents a macrohabitat classification system that has been applied to three large Brazilian floodplains: the forested Amazonian varzeas and igapos, and the savanna floodplains of the upper Paraguai River (Pantanal of Mato Grosso). Examples are provided to demonstrate the applicability of this system in comparative inter- and intra-wetland studies and therefore its utility in assessing environmental changes, including those arising from global climate change. Our approach can also be used to guide the implementation of sustainable management methods and as a focal point for the development of environmental legislation.