The physical environment plays a key role in facilitating the transfer of nutrients and dissolved gases to marine organisms and can alter the rate of delivery of dissolved inorganic carbon. For non-calcifying macroalgae, water motion can influence the physiological and ecological responses to various environmental changes such as ocean acidification (OA). We tested the effects of lowered pH under three different flow speeds on three dominant non-calcifying macroalgal species differing in their carbon-use and are commonly found in the back reefs of Moorea, French Polynesia. Relative growth rates (RGR) of two phaeophytes, Dictyota bartayresiana and Lobophora variegata (HCO3− users), and a rhodophyte, Amansia rhodantha (CO2 user) were measured to examine how the combined effects of OA and flow can affect algal growth. Growth rates were affected independently by pCO2 and flow treatments but there was no significant interactive effect. Additionally, growth rates among species varied within the different flow regimes. Of the three species, L. variegata had the overall greatest increase in RGR across all three flow speeds while A. rhodantha exhibited the greatest negative impact under elevated pCO2 at 0.1 cm·s− 1. These differential responses among algal species demonstrate the importance of flow when examining responses to a changing environment, and if the responses of macroalgae differ based on their carbon-use strategies, it may provide advantages to some macroalgal species in a future, more acidic ocean.