Invasion of zebra mussels (Dreissena polymorpha) can have profound effects on lake ecosystems. We investigated the overall ecological effects after invasion and fast expansion of zebra mussels in eight lakes in Denmark belonging to the same watercourse systems but with different morphological and eutrophication characteristics. A few years after the invasion, most of the lakes had experienced profound changes in lake water quality, e.g. chlorophyll a had been reduced by 18–62% and Secchi depth had increased by 38–171%. Nutrient concentrations also decreased, total phosphorus to 37–64% and total nitrogen to 49–77% of pre-invasion concentrations. Seasonally, differences between both summer and winter phosphorus and nitrogen concentrations diminished, suggesting a change in internal nutrient cycling after the invasion. In most lakes, the abundance of submerged macrophytes rose substantially, and often coverage increased by a factor 10 or more, and the maximum colonization depth increased by up to 5.4 m. Plant species numbers increased markedly in four of the six lakes with macrophyte data. The fish community changed towards higher dominance of potential piscivorous perch and an increase in their body size. The profound effects of zebra mussel invasion may affect lake management and how ecological quality should be interpreted.