Given the need to assess potential effects of rising atmospheric CO2 on aquatic primary productivity, many studies have investigated the physiological mechanisms of inorganic carbon acquisition by a variety of phytoplankton species. Membrane inlet mass spectrometry (MIMS) has become the preferred methodological approach for laboratory experiments, whereas the 14C disequilibrium method has proven to be particularly useful for field studies. In the present investigation, we explicitly compare results of carbon acquisition measurements obtained with both of these approaches. Testing a range of phytoplankton species from different taxa, we show that both methods provide nearly identical results on the contribution of HCO3- and CO2 relative to net carbon fixation. In contrast, although both approaches yielded highly reproducible estimates for extracellular carbonic anhydrase activity, the results differed significantly between the two methods. By directly comparing these two leading methods, we provide experimental confirmation of key assumptions used for data interpretation and discuss possible effects of assay conditions. Our analysis highlights the individual strengths and weaknesses of different approaches.