Obtaining clean and high-quality water free of pathogenic microorganisms is a worldwide challenge. Various techniques have been investigated for achieving an effective removal or inactivation of these pathogenic microorganisms. One of those promising techniques is photocatalysis. In recent years, photocatalytic processes used semiconductors as photocatalysts. They were widely studied as a green and safe technology for water disinfection due to their high efficiency, being non-toxic and inexpensive, and their ability to disinfect a wide range of microorganisms under UV or visible light. In this review, we summarized the inactivation mechanisms of different waterborne pathogenic microorganisms by semiconductor photocatalysts. However, the photocatalytic efficiency of semiconductors photocatalysts, especially titanium dioxide, under visible light is limited and hence needs further improvements. Several strategies have been studied to improve their efficiencies which are briefly discussed in this review. With the developing of nanotechnology, doping with nanomaterials can increase and promote the semiconductor’s photocatalytic efficiency, which can enhance the deactivation or damage of a large number of waterborne pathogenic microorganisms. Here, we present an overview of antimicrobial effects for a wide range of nano-photocatalysts, including titanium dioxide-based, other metal-containing, and metal-free photocatalysts. Promising future directions and challenges for materials research in photocatalytic water disinfection are also concluded in this review.