During the extremely dry period between 2000 and 2003, the water level of Lake Balaton decreased by 82 cm and 80% of the stony littoral, an important habitat for the zebra mussel (Dreissena polymorpha), became dry. A recovery period started in 2004 due to intense precipitation, which increased water levels in the lake. Seasonal and spatial variations of the relative abundance, population density, population structure and biomass of the zebra mussel and the relative abundance of the amphipod Chelicorophium curvispinum were monitored in the period of 2003–2005 at four different shoreline sections and in two different portions (on the bottom and near the surface portion of the rip-rap) of Lake Balaton. Along with these studies, a quantitative survey of mussel larvae found in the plankton and of the abundance of mussel feeding diving ducks were made. As a consequence of the water level fall, on the dried part of the stony littoral, numerous zebra mussel druses perished. Following the dry period in early 2004, the relative abundance of the mussel on the bottom stones was smaller than in 2003 and the bottom community was dominated by C. curvispinum. By the end of 2004 and during 2005, the water level returned to normal and the surfaces of the reinundated stones were conducive to the successful colonization of zebra mussels. Hence, they returned as the dominant fauna in 2005. The stones near the surface might provide a new substrate for the recruitment of zebra mussels, probably offering more suitable substrata for the settlement in 2005 than in 2003. Therefore, the new substrata available in 2005 may have encouraged better and more rapid zebra mussel colonization than before. Zebra mussels may be better competitors for new space than C. curvispinum. A minor change of water-level fluctuation in 2005 and the reduction in population size of the mussel feeding waterfowl could have contributed to the intensive spread of zebra mussel by 2005.