AbstractKey variables in ecosystems tend to operate on widely different time‐scales. These time‐scales become relevant when a disturbance rocks the ecosystem. Here we try to explain the fast dynamics of plankton and nutrients in the water column of floodplain lakes after disturbances (inundations). We take advantage of natural experiments, that is occasional massive overflow of floodplain lakes with river water. We sampled 10 lakes in two floodplains along the Dutch river Waal monthly for 3 years, capturing the impact of three inundation events. The inundations reset the plankton as well as chemical composition of most lakes to largely the same state. While biologically inert macro‐ion data reflected a large and long lasting impact of the river water, dynamics of nutrients, phytoplankton and zooplankton communities between lakes diverged in a few weeks to regimes characteristic for the different lakes. While one spring inundation synchronized plankton dynamics to let the subsequent clear water phase occur at the same moment in different lakes, winter inundations did not have the same effect and apparently dynamics quickly diverged. Our results showed that effects of inundations and other processes that affect the state of the ecosystem should be studied considering the level of the slow components such as the sediment nutrient pool, fish stock and macrophyte communities. Plankton communities and lake water nutrient status give a practically instantaneous reflection of the condition of these slow components. Copyright © 2008 John Wiley & Sons, Ltd.