Water immersion is widely used in physiotherapy and may even improve the functional outcomes of hemiplegic patients after stroke. To investigate the cortical responses to water immersion, functional near-infrared spectroscopy (fNIRS) was used to measure cortical activations in the primary somatosensory area (S1), parietal association area (PAA), supplementary motor area (SMA), and primary motor area (M1). Nine healthy adult males were rested in a sitting position for 15 min with simultaneous measurements of fNIRS, blood pressure, and skin temperature. The fNIRS signal and other physiological parameters were measured under three conditions, the non-immersed condition (baseline control), as the immersion tank was filling with water (pouring water condition), and during sustained water immersion. Each condition lasted for 5 min. The water level was allowed to reach the femur, and during the experiment, room and water temperatures were maintained at 34°C. Oxygenated hemoglobin (oxyHb) concentrations in the S1, PAA, SMA, and M1 remained stable during baseline recording but gradually increased during water pouring and immersion. Significantly higher oxyHb levels were observed in S1 at 20 s after the onset of water immersion condition and in the PAA at 40 s. Subsequently, oxyHb levels in the SMA and M1 increased significantly 100 s after the onset of water immersion condition. In contrast, no significant changes in blood pressure, heart rate, or skin temperature were observed. Water immersion resulted in increased activity in both sensory and motor areas of cortex as measured by non-invasive fNIRS. Water immersion may enhance the efficacy of physical therapy by providing background activation to affected areas of the cortex, thereby enhancing signal processing and learning.