This systematic review and meta-analysis aimed to assess evidence on the effects of aquatic exercise in pregnant women. The search included the following databases: Medline-PubMed, Web of science, PEDro, Scopus and SPORTDiscus databases. Seventeen randomized controlled trials were included (n = 2439, age 20–39 years; 31.30 ± 1.30 years). The systematic review carried out has indicated that aquatic exercise in pregnant women appears to have positive effects on preventing excessive maternal weight gain, improving maternal body image, as well as promoting healthy behavior, decreasing medical leave due to lower back pain during pregnancy, preventing gestational depression by improving maternal glucose tolerance levels, and reducing O’Sullivan test values. The Physiotherapy Evidence Database was used to evaluate the quality of the methodology of the selected studies, which were found to present an average methodological quality (PEDro scale: 5.05 points). Meta-analysis showed that aquatic exercise in pregnant women appears to have positive effects in the prevention of excessive maternal weight gain (mean difference −1.66 kg, 95% CI −2.67 to −0.66) and also to reduce birth weight mean differences (−89.13 g, 95% CI −143.18 to −35.08). The practice of aquatic exercise is appropriate throughout pregnancy. However, more research is needed to build more solid knowledge on the benefits of aquatic physical exercise on physical fitness (endurance, flexibility, agility and strength).