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Fish plays an important role in the human diet, and there is an observed increase in the consumption of fish per capita in Europe. However, intensive growth of industry and agriculture may cause contamination of natural and human-made aquatic environments, and may affect not only the health of fish, but also raise safety concerns with regard to fish used for human consumption. It is well known that fish and fish products are often associated with human diseases. Thus, it is necessary to study the prevalence of pathogens in fish to ensure the safety of fish products and environments. Microbial assessment of fish also gives additional information about the hygienic status of environments, including lakes, rivers, ponds, and fish farms. Detection of pathogenic microorganisms or changes in natural microflora in the water environment could be an important indicator of possible contamination. The aim of this review was to describe and discuss the five most relevant bacterial genera and species linked to aquatic environments—Vibrio spp., Listeria monocytogenes, Yersinia spp., pathogenic Salmonella serovars, and Clostridium botulinum—causing human foodborne diseases.