Marine copepods are an essential live feed for the culture of many marine ornamental fish and other finfish species, yet their production is frequently constrained by contamination from free-living ciliates. To address this challenge, the efficacy of three disinfectants (sodium hypochlorite, iodine, and hydrogen peroxide) was evaluated for ciliate removal in cultures of two copepod species, Parvocalanus crassirostris and Oithona colcarva. Appropriate ranges of disinfectant concentrations and exposure durations were identified through a preliminary trial assessing the toxicity to Euplotes spp. over a 5-min period. Subsequent experiments tested three doses of each disinfectant to quantify ciliate removal success and egg hatch rates for each copepod species. Ciliate presence/absence showed no variation (100% in controls, 0% after disinfection), precluding statistical analysis except for one variable iodine trial, which was analyzed using Fisher’s Exact Test. Hatch and recovery rates were analyzed using binomial GLMMs with treatment as a fixed effect and replicate as a random effect, with Tukey-adjusted pairwise comparisons and α = 0.05. Sodium hypochlorite and hydrogen peroxide consistently removed all ciliates across tested concentrations, whereas iodine only achieved complete removal at the highest dose. The effects on hatch rate differed between species, with hydrogen peroxide producing the highest hatch rates in P. crassirostris (approximately 44 to 46% at 50–100 g/L for one minute) and sodium hypochlorite supporting the highest hatch in O. colcarva (up to 92% at 250 mg/L for one minute). These findings demonstrate that disinfectant performance is species-specific and that species-specific disinfection protocols are warranted to improve the reliability of copepod production in marine aquaculture.