Myxozoan parasites are known pathogens of cultured finfish. Kudoa neurophila n. comb. (Grossel, Dyková, Handlinger & Munday) has historically infected hatchery-produced striped trumpeter, Latris lineata (Forster in Bloch and Schneider), a candidate species for seacage aquaculture in Australia. We examined the efficacy of four water treatment methods to prevent K. neurophila infection in post-larval (paperfish) and juvenile striped trumpeter. Treatments included dose-controlled ultraviolet irradiation [hydro-optic disinfection (HOD)], ozone with conventional UV (ozone), mechanical filtration at 25 μm and then foam fractionation (primary filtration), and 50-μm-filtered sea water (control). In post-larvae (initially 10.3 ± 2.7 g, mean ± SD, 259 days post-hatching, dph), the infection prevalence (PCR test) after 51 days was 93 ± 12% in the control, 100 ± 0% in primary filtration and 0 ± 0% in both ozone and HOD. Likewise, in juveniles (initially 114 ± 18 g, 428 dph), prevalence was 100 ± 0% in the control and primary filtration treatments with no infection detected in ozone and HOD. Concurrently, there was a 50–100% reduction in heterotrophic bacteria and 100% reduction in presumptive Vibrio sp. in sea water HOD and ozone treatments. HOD with a dose of ≥44 mJ cm−2 UV was as effective as ozonation at >700 mV ORP for 10 min, in preventing K. neurophila infection.