Opportunistic premise plumbing pathogens (OPPPs) form a group of microorganisms that normally live in water supply systems and have adapted especially well to the conditions in premise plumbing systems, and as such pose a threat to human health. Since the beginning of the 21st century, this threat has been escalating, and it is becoming increasingly evident that current water disinfection methods fall short in effectively controlling these pathogens. In researching new approaches to this emergency, phototherapy looks promising, especially one that combines photosensitizers, light, and oxygen, which is known as photodynamic inactivation (PDI). This review describes the main characteristics of the recognized (Pseudomonas aeruginosa, Legionella pneumophila, and Mycobacterium avium) and most important emerging OPPPs, and it offers a brief overview of current disinfection methods and their limitations in the fight against OPPPs. The principle and outcomes of PDI with endogenous and, in particular, exogenous photosensitizers are then explained and described through representative examples of PDI on recognized and emerging OPPPs and their biofilms. Finally, the prospects and future directions of PDI research in water disinfection and control of OPPPs are discussed.