Due to climate change the pathogenic bacterium Vibrio vulnificus proliferates along brackish coastlines, posing risks to public health, tourism, and aquaculture. Here we investigated previously suggested regulation measures to reduce the prevalence of V. vulnificus, locally through seagrass and regionally through the reduction of eutrophication and consequential formation of algal blooms. Field samples collected in the summer of 2021 covered the salinity and eutrophication gradients of the Baltic Sea, one of the largest brackish areas worldwide. Physico-, biological- and hydrochemical parameters were measured and variables explaining V. vulnificus occurrence were identified by machine learning. The best V. vulnificus predictors were eutrophication-related features, such as particulate organic carbon and nitrogen, as well as occurrence of potential phytoplankton blooms and associated species. V. vulnificus abundance did not vary significantly between vegetated and non-vegetated areas. Thus, reducing nutrient inputs could be an effective method to control V. vulnificus populations in eutrophied brackish coasts.