Skip the Dip—Avoid the Risk? Integrated Microbiological Water Quality Assessment in the South-Eastern Baltic Sea Coastal Waters

The bathing water microbiome consists of pathogenic and non-pathogenic microorganisms, such as bacteria, viruses, and protozoa. However, the targets of the Bathing Water Directive (2006/7/EC) focus exclusively on fecal pollution. This study aims to investigate fecal indicator bacteria (FIB), naturally thriving cyanobacteria, and Vibrio bacteria in the Lithuanian coastal Baltic Sea and Curonian Lagoon bathing sites, combining information into an integrated microbial risk assessment scheme. The results show that officially monitored indicators, such as FIB, do not exceed the acceptable ‘low’ risk threshold. Simultaneously, cyanobacteria and Vibrio cholerae abundance in the Curonian Lagoon sites reveal a ‘high’ probability of adverse health effects. In coastal bathing sites, a positive correlation was found between Escherichia coli, cyanobacterial harmful algae bloom (cHAB), and V. cholerae, indicating that all target microorganisms may occur at the same time, with consequently high risks for the health of bathers. Therefore, implementing new target organisms in national or even regional bathing water monitoring programs is recommended, in order to safeguard the health of beachgoers.