Quagga and zebra mussels (Dreissena bugensis and D. polymorpha) are highly invasive freshwater mussels in Europe and North America. To better understand the colonization pattern of dreissenids in deep lakes, we studied the settlement of dreissenids along a depth gradient on colonization plates at multiple depths (1-140 m) in the pelagic zone of two recently invaded perialpine lakes—Lake Constance and Lake Geneva. We measured colonization rates every three months over one year on colonization plates deployed in the lake at defined depths. We also assessed long-term population dynamics like abundance and size distribution using photogrammetry of colonization plates. The community of colonising mussels was dominated by quagga mussels with the highest colonization rates and largest sizes occurring above 8 m depth. Colonization rates decreased to almost zero below 30 m. Colonization rates were controlled by variation in environmental conditions and veliger densities across season and depth. Temperature was the most important environmental parameter that influences the colonization. Our results will help to better understand the colonization patterns of invasive quagga mussels in deep lakes.