I examined the physiological response of two marine macrophytes, the brown alga Saccharina latissima and the angiosperm Zostera marina, to water flow in nature and in controlled experiments. Limitation of photosynthesis of both species by the availability of dissolved inorganic carbon (DIC) was increased under low current velocities. Physiological acclimation to low water flow occurred via upregulation of DIC uptake mechanisms in both S. latissima and Z. marina. Both species increased their ability to generate CO2 in the boundary layer by increasing external carbonic anhydrase and in Z. marina by also increasing proton extrusion and photosynthetic capacity. Changes in the xanthophyll-cycle in low-flow grown S. latissima increased non-photochemical quenching, thus reducing photodamage when photosynthesis was limited by DIC uptake. Water flow also affected root length in Z. marina but root length and below ground biomass were also significantly affected by sediment type, an indirect effect of water flow.