Human activities have facilitated the invasion of freshwater ecosystems by a variety of organisms. Especially invasive bivalves such as the quagga mussels, Dreissena bugensis, have the potential to alter ecosystem function as they heavily affect the food web. Quagga mussels occur in high abundance, have a high filtration rate, quickly spread within and between waterbodies via pelagic larvae and colonise various substrates also at greater lake depths. They have invaded various waterbodies on the Northern hemisphere and are continuing to expand their range. Quagga mussels that colonized deeper areas are often thinner and brighter shelled. We analysed 675 quagga mussels using ddRAD sequencing to gain in-depth insights into the genetic population structure of quagga mussels across Central European lakes and across various sites and depth habitats in Lake Constance. We revealed substantial genetic differentiation amongst quagga mussel populations from three unconnected lakes and all populations showed high genetic diversity and effective population size. Our data hence suggests that quagga mussels have arrived independently into the three unconnected lakes and that each invasion likely originated from a distinct and genetically differentiated source population. There was no genetic differentiation amongst quagga mussels across sites and depth habitats within Lake Constance. We also did not identify any convincing candidate loci evidential for adaption along a depth gradient and a transplant experiment showed no indications of adaptation to living in the deep based on investigating growth and survival. Hence, the shallow-water and the deep-water morphotypes seem to be a result of phenotypic plasticity rather than locally adapted to depth. In conclusion, our high-resolution ddRAD approach revealed insight on the independent colonisation of three perialpine lakes and suggests that phenotypic plasticity and marine like reproduction system facilitate the fast spread and colonisation of various depth habitats by the quagga mussel.