Molybdenum (Mo) isotope fractionation has recently been introduced as a new proxy in oceanography and biogeochemistry. It is therefore fundamental to understand the processes controlling Mo partitioning into modern marine environments. This study identifies the availability of dissolved sulfide as the dominant control on overall Mo removal from the water column in euxinic systems. Mo isotopic composition of surface sediments from different localities of the Black Sea demonstrates complete fixation of Mo only below 400 m water depth, above a critical concentration of 11 μmol l−1 aqueous hydrogen sulfide in the bottom water. The Mo isotopic composition of these sediments reflects the homogeneous seawater isotopic composition of 2.3‰. In contrast, significant Mo isotope fractionation into less euxinic sediments is evident at shallower depths in the Black Sea, as well as in temporarily euxinic deeps of the Baltic Sea, consistent with the observed lower maximum sulfide concentrations in the respective water columns. Therefore, Mo isotope signatures in the modern Black Sea constrain the processes responsible for global Mo removal from the ocean by euxinic sediments. Furthermore, models of past ocean anoxia reconstruction have to consider that the seawater Mo isotopic composition is not per se archived in euxinic sediments.