The invasive ctenophore Mnemiopsis leidyi has been reported in various coastal locations in the southern North Sea in the past years. Since 2009, International Bottom Trawl Surveys have recorded this species each winter in open waters. As this species, well-known for its dramatic disturbance of ecosystems, was expected not to be able to overwinter offshore it is crucial to understand its distribution dynamics. Two modelling methods, a quantile regression and a particle tracking model, were used (1) to identify habitats where the invasive ctenophore M. leidyi could survive the North Sea cold winters and (2) to investigate the dispersal of individuals between these different habitats, emphasizing favorable areas where sustainable populations could have been established. Temperature was found to be the crucial factor controlling the winter distribution of M. leidyi in the North Sea. High abundance predictions in winter were associated with low values of temperature, which characterise south-eastern coastal areas and estuaries influenced by riverine runoff. A retention-based M. leidyi population was indicated along the northern Dutch coast and German Bight and a transport-based population offshore from the western Danish coast. Individuals found in the open waters were transported from southern coasts of the North Sea, thus the open water population densities depend on the flux of offspring from these areas. This study provides the first estimates of the overwinter areas of this invasive species over the cold winters in the North Sea. Based on the agreement of habitat and dispersal model results, we conclude that M. leidyi has become established along south-eastern coasts of the North Sea where the environment conditions allows overwintering and it can be retained for later blooms.