This study investigated the effects of different exercise sequences on the neuromuscular adaptations induced by water-based concurrent training in postmenopausal women. Twenty-one healthy postmenopausal women (57.14 ± 2.43 years) were randomly placed into two water-based concurrent training groups: resistance training prior to (RA, n = 10) or after (AR, n = 11) aerobic training. Subjects performed resistance and aerobic training twice a week over 12 weeks, performing both exercise types in the same training session. Upper (elbow flexors) and lower-body (knee extensors) one-repetition maximal test (1RM) and peak torque (PT) (knee extensors) were evaluated. The muscle thickness (MT) of upper (biceps brachii) and lower-body (vastus lateralis) was determined by ultrasonography. Moreover, the maximal and submaximal (neuromuscular economy) electromyographic activity (EMG) of lower-body (vastus lateralis and rectus femoris) was measured. Both RA and AR groups increased the upper- and lower-body 1RM and PT, while the lower-body 1RM increases observed in the RA was greater than AR (34.62 ± 13.51 vs. 14.16 ± 13.68 %). RA and AR showed similar MT increases in upper- and lower-body muscles evaluated. In addition, significant improvements in the maximal and submaximal EMG of lower-body muscles in both RA and AR were found, with no differences between groups. Both exercise sequences in water-based concurrent training presented relevant improvements to promote health and physical fitness in postmenopausal women. However, the exercise sequence resistance-aerobic optimizes the strength gains in lower limbs.