Fossil brachiopod shells are often used as valuable archives to reconstruct paleoenvironmental conditions in deep time. However, biomineralization processes can impact their fidelity as geochemical proxies. Brachiopod shells comprise an outer primary layer, a secondary fibrous layer and sometimes, a tertiary columnar layer. Therefore, it is essential to assess the potential effects of the biomineralization processes in each of the different shell microstructures of modern brachiopods. This study analyses the oxygen isotopic composition together with Li/Ca, Na/Ca Mg/Ca and Sr/Ca data at high spatial (20-50 μm) resolution in seven modern brachiopod species, focusing on differences between the primary, secondary and tertiary layers. In all studied species, δ¹⁸O values of the outer primary layer are consistently out of equilibrium with seawater. Also, this shell layer is enriched in Li, Na, Mg and Sr. Contrary to the primary layer, the innermost secondary layer is near or at oxygen isotopic and elemental equilibrium with ambient seawater. The columnar tertiary shell layer, if present, has the least variable and the heaviest oxygen isotopic composition, within the range of equilibrium values with seawater. This tertiary layer, however, is depleted in minor and trace elements relative to the other shell layers. Thus, the tertiary layer is more suitable for oxygen isotopic studies, whereas the innermost secondary layer of the most mature parts of the shell is the best target in two-layered shells. While we do not observe any clear interspecific relationships between Mg/Ca and Sr/Ca ratios, on one hand, and environmental parameters such as temperature, salinity and pH, on the other hand, there is a positive interspecific relationship between Na/Ca and salinity and a negative interspecific relationship between Li/Ca and temperature, suggesting their potential use as proxies of physicochemical parameters of seawater.