Several studies have demonstrated the positive effects of physical exercise programs on physical and mental health throughout life. It is necessary to know the factors that contribute to the well-being of older adults in order to achieve healthy aging. The aim of this study was to evaluate the relationship between well-being perception and the use of autonomy supportive coaching behaviours across a motivational aquatic resistance interval training program. Thirty-four women over 65 years of age from the province of Alicante, Spain, participated, and were randomly assigned to: motivational aquatic resistance interval training group (MART; age: 69.6 ± 5.01 years, height: 1.62 ± 7.88 m, weight: 75.3 ± 12.8 kg) and control group (CG; age: 67.7 ± 3.60 years, height: 1.54 ± 5.47 m, weight: 66.9 ± 10.2 kg). The MART program was conducted for 14 weeks, with three training sessions/week. The CG did not perform any physical activity during the study. Perception of autonomy support was assessed through the Autonomy-Supportive Coaching Questionnaire (ASCQ), Psychological needs by the Basic Psychological Needs in Exercise Scale (BPNES), Intrinsic motivation to exercise was assessed through Intrinsic Motivation Inventory (IMI) and Perception of Physical Activity by the International physical activity questionnaire (IPAQ). In MART, compared to CG, significant differences were observed in BPNS, IMI and IPAQ questionnaires used, except in the ASCQ. The differences were significant in all three cases in BPNS (p < 0.05 in autonomy and competence and p = 0.001 in relationship with others), obtaining better scores after intervention than previously. As for the IMI scale, significant differences were also obtained in both subscales. The level of physical activity also improved significantly, with higher scores on the IPAQ after the intervention than before (p < 0.001). In conclusion, when practitioners perceive greater well-being, satisfaction of their basic psychological needs, greater self-selection, volition, and autonomy instead of pressure, demand and control, the result is better behaviour with greater psychological well-being, adherence and consequent health benefits.