Introduction The growing research demonstrates that breast cancer surgery and adjuvant radiation therapy greatly improve the long-term results of cancer treatment, overall survival, but leads to negative side-effects including from the respiratory system and quality of life. Aim: To evaluate the impact of a 12-week water program on the respiratory function in breast cancer survivors. Material and methods 68 patients who had survived breast cancer participated in a 12-week physical rehabilitation. Pulmonary function parameters were evaluated in 34 women who performed water program (group A) and 34 women who received Pilates program (group B). Participants of both groups attended 36 rehabilitation sessions over 3 months. Results Based on the results of 12-week rehabilitation, it has been determined that proposed water program is more effective for improvement of pulmonary function in breast cancer survivors at outpatient rehabilitation. It was demonstrated that vital capacity and forced vital capacity were statistically higher by 270 (p<0.001) and 190 ml (p<0.01), respectively in women of group A as compared to the group B. The respiratory minute volume was lower in group A by 1.06 l/min (p>0.05) compared to the group B that indicated about more economical ventilation in rest and increasing the functional reserve of the respiratory system in breast cancer survivors. Conclusions The water-based program appears to be more effective then a Pilates program for improvements in vital capacity, forced vital capacity, maximal voluntary ventilation, and expiratory reserve volume in breast cancer survivors.