Accurately measuring CO2 system variables in the ocean is necessary not only to estimate carbon fluxes, but also to understand changes in seawater chemistry and its effect on marine organisms. Total alkalinity (AT) is one of the most commonly used parameters to characterize the marine CO2 system, but compared to the other measureable CO2 system variables, the measurement of AT necessarily titrates all bases present in seawater, and not just those of interest (carbonate and bicarbonate). While the majority of non-CO2 bases in seawater are identified and easily accounted for, there is extensive evidence for unidentified bases (excess alkalinity, AX) at levels exceeding the uncertainty of the AT measurement. Failure to account for these unidentified bases in a quantitatively meaningful way will lead to errors in interpreting AT as a CO2 system variable. Few methods estimating AX are presented with uncertainty estimates, and none have so far dealt with the uncertainty in the total boron content (BT), the second largest acid-base system in the ocean following the CO2 system. I will describe an open-cell titration approach that can, together with equilibrium modelling, quantify AX as a combination of one or several acid-base systems with apparent total concentration(s) (XT) and acid dissociation constant(s) (KX). The method includes titration of a seawater sample with a strong acid to estimate AT, followed by quantitative removal of CO2. The sample is then titrated with a strong base, and data from this “back-titration” can be used to quantify AX. An uncertainty assessment is provided that includes systematic errors and effects of CO2 contamination, supplemented by colorimetric measurements of BT. This work provides realistic uncertainties of AT measurements made in areas suspected of having a high presence of unidentified acid-base systems, thus contributing to a more accurate assessment of changes in marine CO2 chemistry and speciation in many environments.