We present high-resolution, three-dimensional carbon (δ13C)- and oxygen (δO)-isotope compositions from calcite shells of two modern brachiopod species (Terebratulina crossei and Terebratalia coreanica) and their correlative relationships. δ¹³C and δ¹⁸O values from the secondary shell layer, which constitutes the main body of a brachiopod shell, are in and/or out of the range of δ13C and δ18O values of calcite precipitated in isotopic equilibrium with ambient seawater (equilibrium calcite). The δC and δ18O values of samples from the outermost part of the secondary shell layer show positive correlations. The values of high-growth-rate portions are less than those of low-growth-rate portions; these results are ascribed to a kinetic isotope fractionation effect. Metabolic influences are identified in the isotopic compositions of the low-growth-rate portions for T. coreanica, resulting in decreases in δ13C values compared with those of equilibrium calcite. We illustrate the effects of kinetic isotope fractionation and metabolism on the isotopic compositions of brachiopod shell calcite, which vary among shell portions within a single shell, as well as between the two species. However, appropriate selection of brachiopod taxa and shell portions that reflect the isotopic composition of ambient seawater enables their use as a reliable paleoenvironmental proxy.