Estimates of the effect of increased global atmospheric CO2 levels on oceanic primary productivity depend on the physiological responses of contemporary phytoplankton populations. However, microalgal populations will possibly adapt to rising CO2 levels in such a way that they become genetically different from contemporary populations. The unknown properties of these future populations introduce an undefined error into predictions of C pool dynamics, especially the presence and size of the biological C pump. To address the bias in predictions introduced by evolution, we measured the kinetics of CO2 uptake in populations of Chlamydomonas reinhardtii that had been selected for growth at high CO2 for 1000 generations. Following selection at high CO2, the populations were unable to induce high-affinity CO2 uptake, and one line had a lower rate of net CO2 uptake. We attribute this to conditionally neutral mutations in genes affecting the C concentrating mechanism (CCM). Lower affinity CO2 uptake, in addition to smaller population sizes, results in a significant reduction in net CO2 uptake of about 38% relative to contemporary populations under the same conditions. This shows how predictions about the properties of communities in the future can be influenced by the effect of natural selection.