Extensive bryozoan fossil records date back to the early Ordovician, forming an important part of sedimentary archives, yet the applicability of classical 18‑oxygen thermometry to bryozoan carbonate is still a matter of debate, with mineralogical and biological issues still hindering paleoclimate reconstructions. Complementing other methods (i.e., δ18O, Mg/Ca), clumped-isotope thermometry (Δ47) could provide more accurate paleotemperature estimates and help identify potential biotic factors influencing the isotopic composition of bryozoans. Here we report on the first investigation of clumped-isotope thermometry applied to bryozoan carbonate, spanning a broad range of modern species living in different environments from two localities (Atlantic Ocean and Mediterranean Sea). We confirm that bryozoan δ13C and δ18O records are affected by biotic and abiotic factors susceptible to bias in growth condition estimates. Our Atlantic bryozoans yield Δ47 derived temperatures (T47) consistent with spring/fall seawater temperature (but only after correcting for minor mineralogical effects), reflecting seasonal growth bias or, more likely, moderate isotopic disequilibrium. By contrast, Mediterranean samples display large positive offsets from Δ47 equilibrium values. We propose that this stronger disequilibrium is related to the higher salinity at this site, decreasing Carbonic Anhydrase activity, favoring CO2 hydroxylation over hydration, and slowing down DIC (dissolved inorganic carbon) equilibration reactions at the precipitation site. Our findings highlight how “vital effects” in bryozoans is not only species-specific as often assumed for other biocalcifiers, but could also depend on mineralogy and environmental factors.