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Lake Constance, one of the largest Alpine lakes on the border between Germany, Austria and Switzerland, has undergone extensive changes in the past century. In the 1950-1980s, Lake Constance experienced a phase of severe eutrophication, resulting in significantly increased nutrient-levels. Although the natural trophic state of the lake has been restored, there have been irreversible changes to the communities of aquatic organisms. In addition to eutrophication, climate change and especially the invasion of non-native plant and animal species are endangering natural biodiversity. This leads to changes in the food webs and affect ecosystem functioning in Lake Constance. Specifically the three-spined stickleback (Gasterosteus aculeatus) and Quagga mussel (Dreissena bugensis) cause major problems. The stickleback and Quagga mussel populations have exploded in the last years, with sticklebacks becoming the most abundant pelagic fish species. Quagga is able to settle in all water-depths, which causes problems with water intake pipes and other structures. Furthermore, Quaggas are an important competitor for zooplankton feeding on phytoplankton. We hypothesize that the decline in catch yields and fisheries in Lake Constance is caused, by these two invasive species. We present a large EU funded project (SeeWandel) that i.a. investigates causes and consequences of such invasions for Lake Constance. We present latest results about those invasive species and its consequences for the lake.