Water immersion alters the autonomic nervous system (ANS) response in humans. The effect of water immersion on executive function and ANS responses related to executive function tasks was unknown. Therefore, this study aimed to determine whether water immersion alters ANS response during executive tasks. Fourteen healthy participants performed color–word-matching Stroop tasks before and after non-immersion and water immersion intervention for 15 min in separate sessions. The Stroop task-related skin conductance response (SCR) was measured during every task. In addition, the skin conductance level (SCL) and electrocardiograph signals were measured over the course of the experimental procedure. The main findings of the present study were as follows: 1) water immersion decreased the executive task-related sympathetic nervous response, but did not affect executive function as evaluated by Stroop tasks, and 2) decreased SCL induced by water immersion was maintained for at least 15 min after water immersion. In conclusion, the present results suggest that water immersion decreases the sympathetic skin response during the color–word Stroop test without altering executive performance.