Despite the extensive use of the benthic foraminiferal oxygen isotope composition (δ18O) as a proxy for paleoclimatic reconstructions, uncertainties remain regarding the consistency of interspecies offsets and the environmental factors controlling 18O fractionation. We investigated δ18O offsets of some frequently used Uvigerina, Bulimina, and Cibicidoides species in core top samples from different hydrographic and sedimentary regimes in the South China Sea, Makassar Strait, and Timor Strait/Eastern Indian Ocean. The δ18O values of the epifaunal taxa Cibicidoides mundulus and Cibicidoides wuellerstorfi showed no significant offset in all investigated regions, whereas shallow infaunal Cibicidoides species exhibited higher variability and were less reliable. We found no offsets between species of Uvigerina and Bulimina and assume that these genera can be measured together and/or substituted. Our results show that epifaunal taxa are close to equilibrium with ambient seawater and thus provide more reliable records of past ice volume and/or bottom water temperature variations than infaunal taxa. Offsets among equilibrium calcite, epifaunal taxa, and infaunal taxa are not constant “vital effects” but are influenced by changing gradients in bottom to pore water pH and carbonate ion concentrations that depend on deep-water ventilation and export flux of particulate carbonate and organic carbon. Offsets between epifaunal and infaunal taxa varied between 0.58 and 0.73‰, depending on regional bottom and pore water conditions. Our findings highlight the importance of regional and temporal variations in organic carbon flux/degradation and dissolution of calcite that may lead to slight under- or overestimates of the amplitude of δ18O fluctuations, especially during times of rapidly changing calcite-saturation of bottom and pore water.