We report measurements of the zeta potential on intact limestone samples obtained using the streaming potential method (SPM), supplemented by the more ubiquitous electrophoretic mobility method (EPM). The effect of the potential-determining ions (PDI) Ca, Mg and SO4, and the total ionic strength controlled by NaCl concentration, is investigated over the range typical of natural brines. We find that the zeta potential varies identically and linearly with calcium and magnesium concentration expressed as pCa or pMg. The zeta potential also varies linearly with pSO4. The sensitivity of the zeta potential to PDI concentration, and the IEP expressed as pCa or pMg, both decrease with increasing NaCl concentration. We report considerably lower values of IEP than most previous studies, and the first observed IEP expressed as pMg. The sensitivity of the zeta potential to PDI concentration is lower when measured using the SPM compared to the EPM, owing to the differing location of the shear plane at which the zeta potential is defined. SPM measurements are more appropriate in natural porous samples because they reflect the mineral surfaces that predominantly interact with the adjacent fluids. We demonstrate that special cleaning procedures are required to return samples to a pristine zeta potential after exposure to PDIs. We apply our results to an engineering process: the use of modified injection brine composition to increase oil recovery from carbonate reservoirs. We find a correlation between an increasingly negative zeta potential and increased oil recovery.