During water immersion, we receive several somatosensory input from water, including tactile, pressure and thermal stimuli. In a clinical study involving water immersion, balance ability improved in subjects who rested in a sitting position in water twice a week for five successive weeks. This result suggests that somatosensory input from water may affect the central nervous system, specifically the cerebral cortex. In the present study, we examined the effect of water immersion on short-latency somatosensory evoked potentials (SSEPs) to median nerve stimuli. SSEP recordings were obtained for eight healthy male volunteers. SSEPs were measured at rest under the two environmental conditions: on land and in water. Ambient and water temperatures were set at 30°C under both the conditions. Water was poured up to the axilla level of each subject. A SynAmp amplifier system and the Scan 4.3 software (Neuroscan, El Paso, Texas, USA) were used to record electroencephalographic data. Recordings were obtained from nine scalp electrodes placed at F3/F4, C3/C4, P3/P4, Fz, Cz and Pz according to the 10–20 system. The right median nerve at the wrist was electrically stimulated with the stimulus duration of 0.2 ms at a frequency of 3 Hz. The intensity of the stimulus was fixed at approximately three times the sensory threshold. The following components were consistently recorded in all subjects: P20, N30 and P45 at F3 and Fz, N18, P22, N30 and P45 at C3 and Cz, and N20, P27, N33 and P45 at P3 and Pz. Significant difference between the conditions were found for P45 at C3 and Cz as well as for P27 and P45 at P3 and Pz. We confirmed that water immersion induces significant attenuation (gating) of SSEPs to the median nerve and that it modulates SSEPs known to originate in areas 3b and 1 of SI. We considered SSEP attenuation to be caused by centripetal gating, which suggested that water immersion influences the cortical processing of the somatosensory input.