Carbonate nodules and slabs in late Holocene shelly terrigenous deposits of the modern Fraser River delta (∼49°N) are formed close to the seafloor by precipitation from saline pore waters of mainly fibrous to bladed crystals of high-Mg (∼ 10–20 mol% MgCO3) calcite cement as coalescing isopachous crusts on grains. Previous reports that the cement is low-Mg calcite are not supported by this study. Highly negative δ13C values of − 7 to − 59‰ for the cements indicate that the bulk of their carbonate carbon was derived from the microbiological degradation of organic matter in the deltaic deposits during shallow burial. In particular, the production of biogenic methane (CH4) by anaerobic bacterial fermentation, its upward migration, chemical or biological oxidation to CO2 and neutralization in the near-surface sediment, and diffusion to microenvironments relatively enriched in organic components, are a possible set of conditions influencing the process and sites of carbonate cementation. Methane-derived Mg-calcite appears also to be the major submarine cement in several other modern occurrences of lithified shallow-water terrigenous sands and muds at non-tropical latitudes.