The purpose of this study was to verify the effect of deep-sea water thalassotherapy (DSWTT) on recovery from fatigue and muscle damage. The same exercise program is conducted in general underwater and deep-sea water to confirm the characteristics of deep-sea water through fatigue recovery and muscle damage enzymes. A total of 30 male college students were studied, including 10 belonging to the control group (CG), 10 in the water exercise group (WEG), and 10 in the deep-sea water exercise group (DSWEG). The DSWTT treatment consists of three components—preheating, treatment, and cooling—and the DSWTT program stretches and massages the entire upper body, lower body, back, and the entire body for a total of 25 min in a deep-sea tank. After the DSWTT program, blood tests were conducted to confirm the level of fatigue-related parameters and muscle damage enzymes. Fatigue-related parameters including glucose, lactate, ammonia, and lactate dehydrogenase (LDH), and the levels of muscle damage enzymes such as creatinine kinase (CK) and aspartate aminotransferase (AST) were measured. The results revealed that fatigue had a primary effect (p < 0.001) and exhibited strongly significant interaction (p < 0.001) with lactate, ammonia, and LDH levels, whereas the glucose level remained unchanged. The post hoc results showed a significant decrease in these parameters among DSWEG compared to CG and WEG (p < 0.01). Muscle damage enzymes showed a main effect (p < 0.001) and significant interaction (p < 0.001) with CK and AST (p < 0.001). The post hoc results showed a significant decrease in DSWEG compared with CG and WEG (p < 0.01). In conclusion, the DSWTT program applied to this study showed significant effects on muscle fatigue and muscle damage recovery. When the DSWTT program is applied in hot springs, it can have a positive effect on muscle fatigue and muscle damage recovery and can contribute to improving national health and quality of life. Further studies are needed to investigate DSWTT programs with various research subjects at different program temperatures, exercise times, and frequencies of treatment and exercise.