This study aimed to investigate the effects of two water-based training programs (aerobic and combined) and a non-periodized physical activity program on functional capacity and quality of life (QoL) of elderly women. Forty-one elderly female volunteers (65 ± 4 years) were divided into three groups: aerobic training group (WBA, n = 13), combined training (sequence: resistance/aerobic; WBC; n = 11) and a control group of non-periodized physical activity program (CG, n = 9). The participants performed the water-based trainings twice a week for 12 weeks. The resistance training sets were performed at maximal effort and the aerobic training was performed in the percentage of the heart rate corresponding to the anaerobic threshold (85–110%) determined in an aquatic progressive test. Assessments of QoL perception (WHOQOL-BREF) and functional tests 30-Second Chair Stand, 6-Minute Walk and 8-Foot Up-and-go were performed before and after training. The data were analyzed using Generalized Estimating Equations (GEE), and Bonferroni post-hoc test(α = 0.05). In CG, QoL perception in the physical domain decreased (12 ± 10%) and there was no difference in the other domains. On the other hand, QoL perception was significantly increased in the water-based training groups after the training period in the physical (WBC: 13 ± 16%), psychological (WBA: 9 ± 16%; WBC: 10 ± 11%), social relationships (WBA: 19 ± 42%; WBC: 16 ± 21%) and environmental (WBA: 10 ± 17%; WBC: 16 ± 28%) domains and overall QoL (WBA: 17 ± 22%). No significant difference was observed in the physical domain for WBA and in the overall for WBC. Significant improvements were observed for all groups in the functional tests 30-Second Chair Stand (WBA: 32 ± 11%; WBC: 24 ± 14%; CG: 20 ± 9), 6-Minute Walk (WBA: 10 ± 7%; WBC: 7 ± 6%; CG: 7 ± 5%) and 8-Foot Up-and-go (WBA: 11 ± 5%; WBC: 10 ± 9%; CG: 10 ± 6%). Based on the results observed in this study, it can be concluded that both water-based trainings (aerobic and combined) are effective in improving functional capacity and QoL perception of elderly women. Although non-periodized physical activities seem to be sufficient to positively modify the functional capacity of this population, they are not efficient in improving QoL perception.