Methane‐derived authigenic seep carbonates occur globally along continental margins. These carbonates are important archives to identify seep dynamics, the source of the ascending methane‐enriched fluids together with their timing, and are an important carbon sequestration mechanism. Recently, seep carbonates were discovered in the Levant Basin in the South‐Eastern Mediterranean Sea. To elucidate past seepage activity and dynamics across the basin, different seep carbonate morphologies (chimneys, crusts and pavements) retrieved from the Levant Basin were mapped based on remotely operating vehicle data and analysed using standard sediment petrographic techniques, X‐ray diffraction and stable carbon and oxygen isotope analyses. Carbonate chimneys consist of micrite (δ13CVPDB of ‐10 to +5 ‰) with dispersed barite and dolomite crystals, fan‐shaped aragonite (δ13CVPDB of ‐52 to ‐30 ‰) and high‐magnesium calcite cements, with the latter often growing from low‐magnesium calcite spherules. Botryoidal low‐magnesium calcite cements are forming in small cavities. Carbonate crusts consist of micrite with low‐magnesium calcite breccias, high‐magnesium calcite nodules (δ13CVPDB of ‐35 to ‐20 ‰) and cements, and partially replaced fan‐shaped aragonite cements. Carbonate pavements consist of low‐magnesium calcite microsparite, micritic dolomite and high‐magnesium calcite. Fan‐shaped aragonite is locally present as pore‐lining cement. Iron‐oxides are often seen coating the low‐magnesium calcite, high‐magnesium calcite and dolomite cements. Chimneys and crusts, characterised by high amounts of high‐magnesium calcite and aragonite, are interpreted to have formed through advective methane fluxes. Pavements, with high quantities of dolomite, are explained as the product of diffusive methane flux. Sediment petrographic and geochemical analysis of the different carbonate morphologies and cement phases therein witness distinct modes of ascending fluid fluxes and their mixing with marine porewater and/or seawater during precipitation of the individual phases.