V. cholerae, V. parahaemolyticus and V. vulnificus are potential human pathogens, commonly causing severe infections mostly in tropical or subtropical areas. However, human pathogenic Vibrio are becoming increasingly significant also in temperate waters of northern Europe due to increasing seawater temperatures caused by climate change. Although being pathogens of emerging importance in these waters, currently little is known about the spatiotemporal distribution and environmental dependencies of these species in German coastal waters. Our study covered monthly seawater samples from spring 2015 to spring 2017 in a salinity gradient from the Island Heligoland to the river mouth of the Elbe. On each sampling station different amounts of seawater were filtered on membranes and subjected to APW enrichment (3-MPN). DNA of the extracted biomass was subjected to species specific PCRs targeting V. cholerae, V. parahaemolyticus (toxR) and V. vulnificus (vvhA). To unveil the possible presence of virulent genotypes, further PCRs were performed targeting O1, O139, ctxA (V. cholerae), tdh, trh (V. parahaemolyticus), manIIA and nanA (V. vulnificus). Recurring patterns of investigated Vibrio species during summer seasons were detected. V. cholerae occurrence was restricted to the estuary region in low abundances while V. parahaemolyticus and V. vulnificus occurred throughout the whole sampling transect with up to 4.6 x 103 MPN L-1, respectively. The results showed an increase in pathogenic strain occurrences in the second year of the sampling period. In 2016, 13% of all V. cholerae containing samples were positive for the O139 gene and 28% of V. parahaemolyticus positive samples were carrying the trh gene, both mainly in the estuary region. All V. vulnificus positive samples were manIIA positive and 86% were nanA positive. The presence of pathogenic genes reveals the urgency of a regulated Vibrio surveillance program for a valuable human health risk assessment in the German North Sea, especially due to the expected continuous rise in surface water temperatures.