For decades, red tide control has been recognized as necessary for mitigating financial damage to fish farms. Chemical disinfectants, frequently used for water disinfection, can reduce the risk of red tides on inland fish farms. This study systematically evaluated four different chemical disinfectants (ozone (O3), permanganate (MnO4−), sodium hypochlorite (NaOCl), and hydrogen peroxide (H2O2)) for their potential use in inland fish farms to control red tides by investigating their (i) inactivation efficacy regarding C. polykrikoides, (ii) total residual oxidant and byproduct formation, and (iii) toxicity to fish. The inactivation efficacy of C. polykrikoides cells by chemical disinfectants from highest to lowest followed the order of O3 > MnO4− > NaOCl > H2O2 for different cell density conditions and disinfectant doses. The O3 and NaOCl treatments generated bromate as an oxidation byproduct by reacting with bromide ions in seawater. The acute toxicity tests of the disinfectants for juvenile red sea bream (Pagrus major) showed that 72-h LC50 values were 1.35 (estimated), 0.39, 1.32, and 102.61 mg/L for O3, MnO4−, NaOCl, and H2O2, respectively. Considering the inactivation efficacy, exposure time of residual oxidants, byproduct formation, and toxicity toward fish, H2O2 is suggested as the most practical disinfectant for controlling red tides in inland fish farms.