Phaeophyte macroalgae of the genus Sargassum, including Sargassum muticum, are under investigation as a cultivation crop. Overgrowth or grazing reduces the value and productivity of the crop. This can occur both in the hatchery and during growth at sea, although juvenile stages are especially vulnerable. A decontamination protocol could be used to prevent this. Following a screening procedure, sodium hypochlorite (NaClO) and potassium iodide (KI) were selected for further study. The lethal concentrations for protozoans associated with S. muticum zygotes were 1 % KI, 0.75 % NaClO or a combination of 0.5 % KI and 0.38 % NaClO. A 3-min exposure to these treatments was able to eliminate protozoa from branchlets 20–80 % of the time. NaClO caused large reductions in the operating efficiency of photosystem II (Fq ’/Fm ’), particularly in juveniles (74 ± 17 %), which had still not fully recovered after 17 days. This also halved juvenile density and caused negative growth. One percent KI reduced Fq ’/Fm ’ in adults by 29 ± 11 %, with recovery by day 10. In juveniles, growth was reduced by 65 % and Fq ’/Fm ’ by 61 ± 11 % with recovery after 17 days. A combined treatment of 0.5 % KI and 0.38 % NaClO had far milder effects: reducing adult and juveniles Fq ’/Fm ’ by 6 ± 3 and 34 ± 9 % respectively, with full recovery by day 10. A reduction in juvenile growth was also seen between day 0–10 (32 %); however, size was no different to the control by day 20. This combined treatment is therefore suitable for decontamination of both juveniles and adult S. muticum tissue.