We have evaluated the environmental and biological processes affecting the stable oxygen and carbon isotope composition of live (Rose Bengal stained) and dead (unstained) tests of different benthic foraminiferal species from the western Mediterranean Sea. Samples were retrieved from comparable water depths but contrasting trophic regimes, comprising the meso- to eutrophic Alboran Sea and the oligo- to mesotrophic Mallorca Channel. The recorded isotope signatures mirror the average microhabitat depth of each species and reflect the specific gradients in pore water δ13C of dissolved inorganic carbon (δ13CDIC) and oxygen. Maximum δ13CDIC pore water gradients of up to − 2.3‰ were estimated under the influence of meso- to eutrophic conditions in the Alboran Sea. The δ13C signal of Uvigerina mediterranea reflects the opportunistic behavior of this species as its δ13C is shifted to more negative values at higher organic matter fluxes. Accordingly, the δ13C signal of U. mediterranea appears particularly suitable as a proxy for quantitative reconstructions of past trophic conditions. Previously reported ontogenetic increase of stable isotope values is confirmed for buliminid taxa (genera Uvigerina and Globobulimina), while it is largely absent in rotaliid taxa (genera Cicidides, Cibicidoides, and Melonis). Particularly strong metabolic fractionation is observed in small specimens of Uvigerina peregrina overprinting the pore-water δ13CDIC signal and resulting in steep ontogenetic δ13C gradients. The δ18O values of epifaunal taxa, which thrive under high dissolved oxygen concentrations, and the shallow to intermediate infaunal Melonis barleeanum, are up to 1.2‰ lower relative to equilibrium calcite. In epifaunal taxa, this depletion can be attributed to enhanced fractionation at high concentrations of metabolically utilizable oxygen.