Blooms of Alexandrium spp. are a well-known phenomenon in Northern European waters. While A. tamarense/catenella, and A. pseudogonyaulax have been reported from marine waters, high densities of A. ostenfeldii are mainly observed at lower salinities in North Sea estuaries and the Baltic Sea, suggesting salinity as a driver of Alexandrium species composition and toxin distribution. To investigate this relationship, an oceanographic expedition through a natural salinity gradient was conducted in June 2016 along the coasts of Denmark. Besides hydrographic data, phytoplankton and sediment samples were collected for analyses of Alexandrium spp. cell and cyst abundances, for toxin measurement and cell isolation. Plankton data revealed the predominance of A. pseudogonyaulax at all transect stations while A. ostenfeldii and A. catenella generally contributed a minor fraction to the Alexandrium community. High abundances of A. pseudogonyaulax in the shallow enclosed Limfjord were accompanied by high amounts of goniodomin A (GDA). This toxin was also detected at low abundances along with A. pseudogonyaulax in the North Sea and the Kattegat. Genetic and morphological characterization of established strains showed high similarity of the Northern European population to distant geographic populations. Despite low cell abundances of A. ostenfeldii, different profiles of cycloimines were measured in the North Sea and in the Limfjord. This field survey revealed that salinity alone does not determine Alexandrium species and toxin distribution, but emphasizes the importance of habitat conditions such as proximity to seed banks, shelter, and high nutrient concentrations. The results show that A. pseudogonyaulax has become a prominent member of the Alexandrium spp. community over the past decade in the study area. Analyses of long term monitoring data from the Limfjord confirmed a recent shift to A. pseudogonyaulax dominance. Cyst and toxin records of the species in Kiel Bight suggest a spreading potential into the brackish Baltic Sea, which might lead to an expansion of blooms under future climate conditions.