Magnesium/calcium (Mg/Ca) ratios in two widely used benthic foraminiferal species, Cibicidoides wuellerstorfi and Cibicidoides mundulus (Cibicidoides kullenbergi), picked from global ocean core-tops and from six cores in the North Atlantic Ocean have been measured to investigate Mg/Ca variability, cleaning effect, and influences from bottom water temperature (BWT) and deep water carbonate ion saturation (Δ[CO32−]). Replicate measurements of the two species reveal Mg/Ca variability of 0.07 ± 0.07 mmol/mol. Compared with Mg/Ca in samples cleaned by oxidative cleaning, Mg/Ca ratios are significantly lowered, by 0.10 ± 0.09 mmol/mol, in samples cleaned by reductive cleaning, likely due to preferential leaching during the reductive cleaning step. The cleaning influence is large relative to glacial–interglacial Mg/Ca changes (0.05–0.31 mmol/mol by this study). Regression of core-top data from a wide range of locations show that C. wuellerstorfi Mg/Ca is strongly affected by deep water Δ[CO32−] with a sensitivity of ~ 0.009 mmol/mol per µmol/kg. When BWT is included in regressions, the correlation is slightly more significant with a weak BWT sensitivity on Mg/Ca of between 0.03 ± 0.01 and 0.07 ± 0.02 mmol/mol per °C. Because Δ[CO32−] and BWT co-vary for most core-top samples, an alternate method of separating the two effects was made by comparing glacial to interglacial changes in Mg/Ca from a depth transect of North Atlantic cores where the BWT and carbonate ion histories since the last glacial period have been well constrained. Results from this transect suggest that the BWT effect is < 0.03 mmol/mol per °C, weaker than inferred from the core-top study. Therefore, core-top and down core data suggest that C. wuellerstorfi Mg/Ca is insensitive to BWT changes. The weak BWT effect, when compared with natural variability, complicates the use of Mg/Ca in this species to reconstruct past BWT. Taking all measured samples from various environments into account, C. mundulus Mg/Ca ratios show no correlation with BWT or deep water Δ[CO32−].