This review is aimed at the actions of radical oxygen species (ROS) produced during the photocatalysis reaction on the different biomolecules composing the microorganisms, as well as the presentation and development of the key operational parameters influencing the efficiency of the photocatalytic treatment in the context of saltwater applications. Our study focuses on the case of heterogeneous photocatalysis, one of the advanced oxidation processes (AOP). This work highlights the importance of the analytical composition of the water (pH, salt, dissolved organic matter.) on the catalyst/target interactions. Similarly, the structural composition of microorganisms (cell wall biomolecules) also plays a key role in the sensitivity to the photocatalysis process, and to a lesser extent, their metabolism also has an impact on their resistance. Another important point of our work is that it highlights the fact that to date, there is no standardization in the way results from the literature are reported, making it extremely difficult to compare data for the purpose of evaluating different processes. Finally, our work underlines that photocatalysis is particularly promising for bio-securing applications like the decontamination of seawater in aquaculture via the treatment of tanks and closed aquariums, as well as for the shipping industry via the treatment of ballast water.