Hot springs have long been used for medical purposes throughout the world. However, their health effects are still largely unknown. Therefore, we aimed to examine the physical and mental effects of hot spring spa-bathing habits throughout Japan. We conducted a new online questionnaire survey throughout Japan that included questions on spa-bathing behavior, disease prevalence, subjective satisfaction, and lifestyle habits. To understand regional differences, we used previously reported questionnaire data as a comparison. Regarding mental effects, the results showed a significant positive correlation between spa-bathing habits and subjective satisfaction. Moreover, 2% of life satisfaction was explained by spa-bathing habits in the regression model. Regarding physical effects, we found a significant reduction in the odds ratio of hypertension among spa bathers in two populations: elderly people nationwide and elderly people in Beppu. In addition, among elderly individuals in Beppu, the odds ratios of depression and hyperlipidemia were significantly lower among spa bathers, suggesting that there may be differences in the effects of hot springs between regions. This study revealed that hot spring spa-bathing habits positively impacted both physical and mental health. Our findings suggest that spa bathing could improve health status, especially among elderly individuals, by preventing hypertension and improving mental health.