Alternative stable states in shallow lakes have received much attention over the past decades, but less is known about transient dynamics of such lakes in the face of stochastic perturbations such as incidental extremes in water levels driven by climatic variability. Here, we report on the ecosystem dynamics of 70 lakes in the floodplains of the Lower Rhine in The Netherlands from 1999 to 2004. In any particular year, most lakes were either in a macrophyte-dominated clear state or in a contrasting state with turbid water and sparse submerged macrophyte cover. Macrophyte dominance was positively related to the occurrence of drawdown, and negatively to lake surface area and mean depth. We did not find a relation with nutrient levels. Remarkably, shifts between the two contrasting states were common, and episodes of low water levels appear to be an important external driver. A dry period before our study and the exceptionally dry summer of 2003 caused widespread drawdown of floodplain lakes, resulting in establishment of submerged macrophytes in the next year upon refill. In the 4 years without drawdown, many lakes returned to a macrophyte-poor turbid state. Although some lakes turned turbid again quickly, others took several years to shift into the turbid state. A model analysis suggests that such prolonged transient vegetated states may be explained by the fact that the system dynamics slow down in the vicinity of the “almost stable” macrophyte-dominated state. Such a “ghost” of an equilibrium causes the system to stick around that state relatively long before slipping into the only true stable state. Our results support the idea that transient dynamics rather than equilibrium may be the key to understanding the overall state of some ecosystems. A practical implication of our findings is that artificial stabilization of the water level in shallow lakes may have been an important factor aggravating the permanent loss of submerged macrophytes due to cultural eutrophication.