Aquatic exercise is being increasingly recommended for healthy individuals as well as people with some special health conditions. A systematic review with meta-analysis was performed to synthesize and analyze data on the effects of water-based training (WT) programs on health status and physical fitness of healthy adults and adults with diseases to develop useful recommendations for health and sports professionals. We searched three databases (PubMed, Web of Science, and Scopus) up to June 2021 for randomized trials that examined WT in adults. A total of 62 studies were included, of which 26 involved only healthy individuals and 36 focused on adults with chronic diseases. In the healthy group, the effects of WT on strength, balance, and cardiorespiratory fitness were beneficial, indicating the usefulness of performing WT for at least 12 weeks (2–3x/week, 46–65 min/session). Among adults with diseases, improvements were observed in patients with fibromyalgia (in balance and cardiorespiratory fitness), bone diseases (pain, balance, flexibility, and strength), coronary artery disease (strength and anthropometry), hypertension (quality of life), stroke (quality of life), diabetes (balance and quality of life), multiple sclerosis (quality of life and balance), and Parkinson's disease (pain, gait, cardiorespiratory fitness, and quality of life). Research is required to determine the effects of WT on patients with heart disease, especially coronary artery disease. In adults with chronic disease, benefits in physical fitness and/or other health-related measures were mainly observed after 8–16 weeks of training. WT is an effective physical activity when the intention is to enhance health and physical fitness in healthy adults and adults with chronic diseases.