Stable carbon and oxygen isotopic compositions (δ¹³C and δ¹⁸O) of benthic foraminiferal carbonate shells have been used to reconstruct past bottom-water environments. However, the details of factors controlling the isotopic disequilibrium between the shells and the surrounding bottom seawater (so-called the "vital effect") are still ambiguous. In this study, we analyzed the isotopic composition of individual benthic foraminifera of multiple species by using a customized high-precision analytical system, and found that the magnitude of the isotopic disequilibrium between benthic foraminiferal shell and the surrounding bottom seawater (δ¹³C_DIC and δ¹⁸O_water) in different species is correlated with inter-individual isotopic variations. As a result, we can choose suitable species as bottom-water proxies by using the inter-individual isotopic variations. In addition, by using the simplified interpretation of the inter-individual and inter-species isotopic variations established in this study, we could reconstruct the δ¹³C values of dissolved inorganic carbon in bottom water by correcting foraminiferal isotopic compositions for the isotopic shift resulting from the isotopic effects (vital effect, microhabitat effect, and many other reported isotopic effects). Our findings will allow the use of isotope data for benthic foraminifera as more reliable proxies for reconstructing past bottom-water conditions and evaluating global carbon cycling.