Purpose. To compare the effects of aquatic and land plyometric training on the vertical jump (VJ) and delayed onset muscle soreness (DOMS) in soccer players. Methods. Twenty-four male soccer players aged 16-18 years (16.53 ± 0.5 years) were randomly divided into three groups: aquatic plyometric training (APT) (n = 8; age: 16.4 ± 0.4 years; body mass: 68.3 ± 7.54 kg; height: 179.75 ± 8.13 cm); land plyometric training (LPT) (n = 8; age: 16.5 ± 0.5 years; body mass: 68.2 ± 7.8 kg; height: 177.0 ± 7.4 cm); and control group (n = 8; age: 16.7 ± 0.6 years; body mass: 61.2 ± 6.5 kg; height: 171.43 ± 5.75 cm), not performing any jump program. An identical training program was applied for 6 weeks, totalling 944 jumps. The VJ was evaluated on a leap jump platform and the Visual Analogue Scale measured the change in DOMS perception. Results. There was a significant increase in the VJ height in both experimental groups (LPT and APT) (p < 0.05). A significant reduction in DOMS perception was verified for the APT group in comparison with the LPT group (p < 0.05) between the first and last week of training. The foot contact time significantly decreased (p < 0.05) in the APT group from pre- to posttest. Significant improvements (p < 0.05) were observed in the flight time and jump speed from pre- to post-test in both LPT and APT groups. Conclusions. APT can increase the VJ height and reduce DOMS perception in soccer players.