This study aims to undertake hydroxyl (.OH) radical-based preliminary investigations with a view to utilising seawater as a viable alternative to freshwater for the treatment of amoebic gill disease (AGD) in aquaculture industries. The study presents in vitro viability studies of clonal amoebae species to examine the effects of .OH radicals on both parasites and hosts. The study also assesses the toxicity to Chinook salmon cell lines (CHSE-214) in freshwater and 35 ppt seawater via continuous dosing of 35 mM .OH radicals and hydrogen peroxide (H2O2) for 1.5 to 4 hr, separately at 18°C and 15°C. Comparatively high viability of CHSE-214 (60% in .OH and 50% in H2O2) for a prolonged treatment of up to 4 hr in seawater at 15°C indicates suitability of low seawater temperature while using either .OH or H2O2 during bathing. The viability of CHSE-214 remained relatively stable in seawater (55%–60% in .OH and 50%–60% in H2O2), at both temperatures of 18°C and 15°C. However, at 15°C, a drastic reduction of viability of CHSE-214 in freshwater (from 80% to 48% in .OH and from 70% to 58% in H2O2) has indicated high variations in toxicity levels in freshwater at low temperature. Using DNA staining agents in flow cytometry, the in vitro viability study results in >22.5% mortality of clonal Neoparamoeba perurans (NP), an AGD causative agent, in 35 ppt seawater containing 35 mM .OH radicals via one-off dosing for 1 hour at 15°C. In addition, fast radical consumption is more pronounced in the case of .OH radicals as compared to H2O2 in both freshwater and seawater due to extreme reactivity of the former. Hence, this study suggests that .OH radicals are detrimental to the viability of NP in seawater, and thereby, establishes grounds for further in vivo investigations of using seawater supplemented with continuous dosing of .OH radicals for Atlantic salmon bathing as a treatment of AGD.