The shell material of marine benthic bivalves provides a sensitive archive of water chemistry immediately above the sediment–water interface, which in turn is affected by sedimentary geochemistry and redox reactions. Sulfate has a major controlling effect on sedimentary carbon cycling, particularly the processes of methane production and oxidation, with lower concentrations of sulfate likely resulting in an increase in sedimentary methane production. Whilst it is accepted that ocean sulfate varied markedly across the Phanerozoic, evidence of changes in methane production in sediments has so far been lacking. There is potential for the oxidation products of sedimentary methane to be preserved and detected in marine fossils. Here we present the results of high resolution carbonate isotope records from two taxa of well-preserved shallow-infaunal bivalve (Lahillia and Cucullaea) collected from the marine shelf succession across the Cretaceous–Paleogene (K–Pg) boundary in Seymour Island, Antarctica. The succession has pre-existing subtle indications of more abundant methane, and the time period is characterized by much lower marine sulfate concentrations than modern.These shell carbonate–carbon isotope records vary widely: at one extreme, shells have typical average values and small ranges compatible with a contemporaneous marine dissolved inorganic carbon (DIC) source and modern-style sedimentary carbon cycling. At the other, the shells have large-amplitude annual cycles of carbon isotopic variability of up to 23.8‰ within a single year of growth and shell carbonate δ13C compositions as negative as −34‰. Shells with these increased ranges and unusually negative values are found at discrete intervals and across both bivalve taxa. The contribution of methane required to explain the most negative carbonate–carbon isotopic values in the bivalve shells is extremely high (between 30 to 85% of bottom-water DIC based on mass balance calculations). Records of organic-carbon isotopes from the same succession remained between −26.1 and −21.7‰ throughout, suggesting that methane influence was restricted to bottom-waters. A lack of authigenic carbonate in the section indicates that methane oxidation progressed aerobically and may have provided a significant driver for transient bottom water de-oxygenation.Where methane addition is indicated, the seasonal sensitivity precludes control by methane hydrates. We argue that these data represent the increased importance and sensitivity of methanogenesis in the sediments, enabled by lower ocean sulfate concentrations during the Late Cretaceous. The tendency towards a more dynamic role for marine methane production and oxidation is likely to apply to other times of low marine sulfate in Earth's history.