Bacterial infections account for one of the major causes of disease losses in aquaculture. Antibiotics are the most common method used to mitigate these infections, but over the last few decades this has given rise to antimicrobial resistance so finding alternatives to these treatments is imperative. Here we report a drug-free cost-effective method for rapid and safe water disinfection. A pair of laser-induced graphene (LIG) electrodes charged with low voltage (2 V) rapidly inactivated Escherichia coli and Bacillus subtilis in various circulating saltwater systems without significant changes in water quality parameters (pH, dissolved oxygen, and temperature). Bacterial inactivation was enhanced with increasing water salinity during electrochemical disinfection using LIG electrodes. Meanwhile, the concentrations of oxidants such as hydrogen peroxide and ozone were generally low regardless of water salinities, and chlorine was not detectable during the treatments. No health impacts were observed in Japanese medaka exposed to eight days of 1 h LIG electrochemical treatments applied twice a day. Our findings suggest that rapid disinfection of saltwater could be achieved using LIG electrodes without negative health impacts on fish, providing potentially an efficient and safe method for controlling bacteria in saltwater systems.