Global fish consumption is expected to reach 194 million tonnes by 2026 (FAO, 2017). As a result, careful consideration must be given to the environmental impacts of aquaculture expansion, including potential pollution of receiving waters with effluent from the growth and processing of fish products. The main aim of this study was to improve fish processing wastewater treatment by reducing the dissolved inorganic nitrogen concentration and chemical oxygen demand using bioaugmentation, through the application of newly isolated halotolerant, protease-producing bacteria. Five halotolerant bacteria strains were isolated and identified as Marinirhabdus sp., Vibrio sp., Alteromonas sp., Alteromonas macleodii, and Marinobacter hydrocarbonoclasticus based on 16S rRNA sequence phylogenetic analysis. Marinirhabdus sp. and Marinobacter hydrocarbonoclasticus showed significantly higher efficiencies of COD and nitrate, nitrite and ammonium removal compared with the non-bioaugmented control. The COD and nitrogen concentration in fish wastewater treated with Marinirhabdus sp. and Marinobacter hydrocarbonoclasticus were 93 mg L−1, 95 mg L−1, and 66.7 mg L−1, 53.3 mg L−1, respectively, with a decrease in total nitrogen synchronous with the degradation of nitrate, nitrite, and ammonium. This work demonstrated that wastewater bioaugmentation represents an effective treatment for saline, fish processing wastewater, and could be used as a robust method for the removal of organic matter and nitrogen in saline fish wastewater.