We investigate the redox-sensitive isotope system of molybdenum (Mo) in marine carbonates to evaluate their potential as archive of the Mo isotopic composition of coeval seawater. We present Mo isotope data (delta(98/95)Mo) of modern skeletal and non-skeletal carbonates as well as a variety of precipitates from the mid and late Carboniferous. The external reproducibility is determined by repeated analyses of two commercially available carbonate standards. The resulting uncertainty of the low concentration samples is +/-0.1 parts per thousand (2 sigma). Analysis of modern ooid sands from the Bahamas shows a consistently heavy Mo isotopic composition (delta(98/95)Mo between 2 and 2.2 parts per thousand), approaching modern mean seawater values (delta(98/95)Mo = 2.3 parts per thousand +/- 0.1 parts per thousand (2 sigma). This suggests that isotope fractionation during Mo uptake into non-skeletal carbonate precipitates is small. In contrast, modern skeletal carbonates show variable isotopic compositions (0.1 to 2.2 parts per thousand) which suggests a biologically controlled fractionation process. The varying Mo signatures found in Carboniferous cement phases point to a strong response to local changes in fluid composition from which they precipitated. Overall, we recognized three important factors to cause an offset relative to ocean water: Mo derived from skeletal components, input of detrital Mo and admixture of light, hydroxide derived Mo via diagenetic fluids. All of these factors cause a lighter Mo isotopic composition relative to seawater. Due to the apparent small isotope fractionation during Mo uptake into non-skeletal carbonates, their delta(98/95)Mo closely reflects the ambient fluid composition. From these results we conclude that carbonates represent a promising new tool to characterize the water mass Mo isotopic composition of marine paleo-environments.