Acidic freshwater habitats disrupt ion-homeostasis in fishes, yet the often acidic waters of the Mekong host the second highest diversity of freshwater fish in the world. To investigate how five Mekong fish species tolerate water acidity, we measured: time to loss of equilibrium (LOE) at sustained (4 days) low pH (3.5) and net ion flux in acute low pH (3.5 and 3) in Chitala ornata, Pangasianodon hypophthalmus, Osphronemus goramy, Trichogaster pectoralis, and Monopterus albus. Our sustained low pH exposures revealed that C. ornata was least tolerant, P. hypophthalmus and M. albus were moderately tolerant, and O. goramy and T. pectoralis were highly tolerant to low pH. In general, net ion loss in acute low pH exposures was greatest in species with the shortest time to LOE in the sustained low pH exposure. We also explored how low water [Ca2+] (relative to current Mekong levels) affected ion flux at low water pH in the least tolerant C. ornata and highly tolerant T. pectoralis. In C. ornata, low water Ca2+ (56 ± 1 μmol L−1) increased net ion loss relative to high Ca2+ (342 ± 3 μmol L−1) water while no effect was observed in T. pectoralis. Finally, we find that T. pectoralis is among the most acid-tolerant fish species examined to date.