Introduction: Many women change their lifestyles and habits when they become pregnant, to avoid potentially harmful effects to themselves and their babies. This is especially so with respect to physical exercise, which is often greatly reduced due to ignorance of the benefits it provides during pregnancy. Aim: To evaluate the prevalence of spontaneous birth among women who participated in a water-based physical exercise program. Methods: A randomized clinical trial was conducted with a sample of 129 pregnant women (Control Group, CG = 64; Exercise Group, EG = 65). A physical exercise protocol, specifically designed for pregnant women, was created and applied. Those in the EG performed 60 min exercise sessions, three times per week for 17 weeks. The participants in the CG received routine check-ups and advice throughout their pregnancy. Findings: The women in the EG presented better results for the onset of spontaneous birth (OR = 2.060 (0.980–4.332)) and for neonate Apgar score of 10 at five minutes (OR = 8.53 (3.60–20.17)). Those who had normal weight at the start of pregnancy achieved better results for spontaneous delivery (OR = 2.099 (1.017–4.335)) than those with overweight/obesity. The rate of caesarean delivery was higher in the women with overweight/obesity (OR = 3.570 ((1.226–10.397)) than in those with normal weight. Conclusions: In our study, the women who followed the water-based exercise program gained less weight during pregnancy, which facilitated a better rate of spontaneous, non-instrumental childbirth, together with a better Apgar test score at five minutes.