This study aims to isolate the freshwater fish–derived potential probiotics and evaluate their beneficial effects on the growth, immune response, and disease resistance of juvenile zebrafish (Danio rerio). Herein, three strains (Leuconostoc mesenteroides GL-5, Weissella hellenica GJ-1, and Pediococcus claussenii GJ-3) were identified with antagonistic activity against fish pathogens, high tolerance to 0.1% bile salt, and good hydrophobicity. As the model, zebrafish (15 days post-fertilization, dpf) were fed with a basal diet (control) supplemented with GL-5, GJ-1, GJ-3, heat-killed Leuconostoc mesenteroides GL-5*, and commercial probiotics (positive control) at a concentration of 1 × 107 CFU/mL for 4 weeks. Compared with the GL-5* (36.35 ± 2.03 mg fish−1) and control (37.31 ± 1.91 mg fish−1) groups, the GL-5 (58.15 ± 2.58 mg fish−1), GJ-1 (69.55 ± 3.85 mg fish−1), GJ-3 (62.90 ± 2.99 mg fish−1), and commercial probiotic (62.03 ± 2.68 mg fish−1) treatment were found to significantly promote the growth of zebrafish. Compared to the control group challenged by immersion with 1 × 107 CFU/mL Aeromonas hydrophila, the GJ-3 and positive groups showed the highest transcript levels of IL-1β and TNF-α at 8 h post-challenge (P < 0.05). The survival rates (80%) of the GJ-3 and commercial probiotic–fed groups were significantly higher than that of the control group (50%) at 32 h post-challenge (P < 0.05). Therefore, Pediococcus claussenii GJ-3 can be considered a potential probiotic for reducing the use of antibiotics and preventing bacterial diseases in fish.