The emergence of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in the environment has created obstacles when treating infectious diseases with antibiotics. Wastewater treatment plants (WWTPs) serve as reservoirs for ARB and ARGs and can disseminate them into the environment. It is important to understand and address these risks. Generally, professional disinfection processes have been used in WWTPs to disinfect the target water body, with the goal of eliminating pathogenic microorganisms in the water. However, ARGs are not generally considered, and antibiotic resistance has spread and developed through horizontal gene transfer (HGT). This Review provides a detailed overview of the application progress of different traditional and new disinfection technologies in removing ARB and ARGs, mainly focusing on the bacterial inactivation mechanisms of chlorination, ozonation, ultraviolet (UV) (including UVA, UVB, and UVC), sunlight, sunlight-dissolved organic matter (DOM), and photocatalysis (PC)/photoelectrocatalysis (PEC). In addition, this Review also focuses on the disinfection technology involved in the transfer of ARGs and clarifies the underlying transfer mechanisms in water environments. Furthermore, by linking the mechanisms of bacterial inactivation, the Review describes how SOS response and cell membrane permeability may be the key step in the conjugation, transformation, and transduction of ARGs. Finally, given the applications and current problems associated with traditional water disinfection technologies and light-based disinfection technologies in removing and controlling ARB and ARGs, this Review describes the current challenges and opportunities to facilitate the development of future disinfection technologies. The Review also highlights future research directions related to ARG transmission control.