Water exercise has various health benefits. However, effects of low-intensity water exercise program, frequently conducted as a health promotion activity, on high frequency component of heart rate variability (HF, an index of cardiovagal activity and a predictor of future cardiovascular disease) has been unexplored. To investigate acute effects of a low-intensity water exercise program on cardiovagal activity, 35 young healthy men participated in this study as a part of the water exercise group (15 min of walking, 10 min of jogging, and 10 min of supine floating) or the control group (35 min of sitting at rest on land). Heart rate during walking, jogging, and floating in water were 88±13, 104±19, and 73±14 bpm, respectively. Ratings of perceived exertion (Borg’s 6—20 scale) were 9±2, 10±2, and 7±2, respectively. Before the low-intensity water exercise program or 35-min sitting rest, there were no intergroup differences in natural logarithm of HF (lnHF), the ratio of low to high frequency component of heart rate variability (LF/HF), heart rate, blood pressure, sublingual temperature, and salivary amylase activity. An interaction between time and group was found in lnHF (P = 0.01); lnHF was greater 15 min and 30 min after versus before the program in the water exercise group, whereas there were no differences in the control group. There were no interactions in LF/HF, heart rate, blood pressure, sublingual temperature, and salivary amylase activity. These results suggest that the low-intensity water exercise program consists of walking, jogging, and supine floating acutely enhances cardiovagal activity.