BACKGROUNDThe uncontrolled discharge of untreated ballast water, which is essential for a ship's optimal operation, is one of the major causes of sea environmental pollution by shipping. Among the disinfection methods available for ballast water treatment, ozonation is a commonly used method, but its performance is limited by the rapid ozone auto‐decomposition rate. Nanobubbles (NBs) technology has attracted much scientific interest as it is characterized by a long residence time in the aqueous phase and a high surface area; therefore, ozone nanobubbles (OzNBs) are expected to enhance disinfection capacity and residual activity. The present study was designed to provide further insight into the inactivation of heterotrophic bacteria in saline water and to examine the use of OzNBs for disinfection of saline water.RESULTSThe survival rate of Escherichia coli (E. coli), which was used as indicator microorganism, along with the ozone consumption at different salinities (1.5, 4, 8 and 15 PSU) and bacterial concentrations (107, 106, and 105 CFU mL−1) with and without supplementation of OzNBs were investigated. The results indicated a statistical difference in the residual concentration of total residual oxidants (TRO) with the presence of OzNBs at salinity level 1.5 PSU and at 4 PSU only at the lowest bacterial content. At a low salinity and high bacterial concentration, the concentration of TRO was 6‐fold higher in the presence of OzNBs.CONCLUSIONThe salinity of water has a strong impact on the residual concentration of ozone. When salinity is increased, ozone reacts more rapidly with the bromide and chloride ions. The use of OzNBs exhibited a greater disinfection performance and higher residual activity. © 2023 The Authors. Journal of Chemical Technology and Biotechnology published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry (SCI).