Serpentinization of ultramafic rocks in the sea and on land leads to the generation of alkaline fluids rich in molecular hydrogen (H2) and methane (CH4) that favour the formation of carbonate mineralization, such as veins in the sub-seafloor, seafloor carbonate chimneys and terrestrial hyperalkaline spring deposits. Examples of this type of seawater–rock interaction and the formation of serpentinization-derived carbonates in a shallow-marine environment are scarce, and almost entirely lacking in the geological record. Here we present evidence for serpentinization-induced fluid seepage in shallow-marine sedimentary rocks from the Upper Cretaceous (upper Campanian to lower Maastrichtian) Qahlah Formation at Jebel Huwayyah, United Arab Emirates. The research object is a metre-scale structure (the Jebel Huwayyah Mound) formed of calcite-cemented sand grains, which formed a positive seafloor feature. The Jebel Huwayyah Mound contains numerous vertically orientated fluid conduits containing two main phases of calcite cement. We use C and O stable isotopes and elemental composition to reconstruct the fluids from which these cements precipitated and infer that the fluids consisted of variable mixtures of seawater and fluids derived from serpentinization of the underlying Semail Ophiolite. Based on their negative δ13C values, hardgrounds in the same section as the Jebel Huwayyah Mound may also have had a similar origin. The Jebel Huwayyah Mound shows that serpentinization of the Semail Ophiolite by seawater occurred very soon after obduction and marine transgression, a process that continued through to the Miocene, and, with interaction of meteoric water, up to the present day.