Photocatalysis has received ever‐growing attention as a promising alternative to traditional water treatment technologies for waterborne biohazard inactivation. Due to unique optical, electronic, physicochemical properties and feasibility of functional architecture assembly, two‐dimensional (2D) nanomaterials have become important in developing novel photocatalysts. This review summarizes the recent progress in configuring nanostructures with 2D materials as building blocks for photocatalytic water disinfection. In this review, five categories of 2D nanomaterials, that is, graphene, graphitic carbon nitride, 2D metal oxides and metallates, metal oxyhalides and transition metal dichalcogenides, for photocatalytic pathogen inactivation are introduced. First, the synthesis process, nanostructure engineering and disinfection performance of 2D‐based photocatalysts are reviewed in categories. In the following section, the bacteria destruction mechanism based on the generation and roles of reactive species (RSs) is presented. Moreover, the effects of the chemical characteristics of the water matrix on photocatalytic bactericidal performance are discussed. Finally, the challenges regarding the development and application of 2D‐based photocatalysts for highly efficient water sterilization are highlighted. © 2018 Society of Chemical Industry