The number of
Vibrio
-related infections in humans, e.g., by
Vibrio vulnificus
, has increased along the coasts of the Baltic Sea. Due to climate change, vibriosis risk is expected to increase. It is, therefore, pertinent to design a strategy for mitigation of the vibriosis threat in the Baltic Sea area, but a prerequisite is to identify the environmental conditions promoting the occurrence of pathogenic
Vibrio
spp., like
V. vulnificus
. To address this, we sampled three coastal Baltic sites in Finland, Germany, and Denmark with salinities between 6 and 21 from May to October 2022. The absolute and relative abundances of
Vibrio
spp. and
V. vulnificus
in water were compared to environmental conditions, including the presence of the eelgrass
Zostera marina
, which has been suggested to reduce pathogenic
Vibrio
species abundance. In the water column,
V. vulnificus
only occurred at the German station between July and August at salinity 8.1–11.2. Temperature and phosphate (PO
4
3–
) were identified as the most influencing factors for
Vibrio
spp. and
V. vulnificus
. The accumulation of
Vibrio
spp. in the sediment and the co-occurrence with sediment bacteria in the water column indicate that sediment resuspension contributed to
V. vulnificus
abundance. Interestingly,
V. vulnificus
co-occurred with specific cyanobacteria taxa, as well as specific bacteria associated with cyanobacteria. Although we found no reduction in
Vibrio
spp. or
V. vulnificus
associated with eelgrass beds, our study underscores the importance of extended heatwaves and sediment resuspension, which may elevate the availability of PO
4
3–
, for
Vibrio
species levels at intermediate salinities in the Baltic Sea.
IMPORTANCE
Elevated sea surface temperatures are increasing the prevalence of pathogenic
Vibrio
at higher latitudes. The recent increase in
Vibrio
-related wound infections and deaths along the Baltic coasts is, therefore, of serious health concern. We used culture-independent data generated from three Baltic coastal sites in Denmark, Germany, and Finland from May to October (2022), with a special focus on
Vibrio vulnificus
, and combined it with environmental data. Our temporal model shows that temperature, combined with sediment resuspension, drives the prevalence of
V. vulnificus
at intermediate salinities in the coastal Baltic Sea.