The study investigated the effects of different intrasession exercise sequences on the cardiorespiratory and neuromuscular adaptations induced by water-based concurrent training in young subjects. Twenty-six healthy young women (25.1 ± 2.9 years) were placed into 2 water-based concurrent training groups: resistance before (RA, n = 13) or after (AR, n = 13) aerobic training. Subjects trained resistance and aerobic training during 12 weeks, 2 times per week performing both exercise types in the same training session. Peak oxygen uptake (V[Combining Dot Above]O2peak), rate of force development (RFD) obtained during an isometric peak torque knee extension protocol, jump height, and neuromuscular economy (normalized electromyography at 80% of pretraining knee extension isometric peak torque) in young women were determined. After training, there was a significant increase (p < 0.001) in both RA and AR in the V[Combining Dot Above]O2peak, with no differences between groups (7 vs. 5%). The maximal isometric knee extension RFD showed significant increases (p = 0.003) after training (RA: 19 vs. AR: 30%), and both groups presented similar gains. In addition, the countermovement jump height also increased (p = 0.034) after training (RA: 5% vs. AR: 6%), with no difference between groups. After training, there were significant improvements on vastus lateralis (p < 0.001) (RA: -13% vs. AR: -20%) and rectus femoris (p = 0.025) (RA: -17% vs. AR: -7%) neuromuscular economy, with no difference between groups. In conclusion, 12 weeks of water-based concurrent training improved the peak oxygen uptake, RFD, jump height, and neuromuscular economy in young women independent from the intrasession exercise sequence.