ABSTRACT A comprehensive approach using palaeontology, petrography, stable isotope geochemistry and biomarker analyses was applied to the study of seven small methane-seep carbonate deposits. These deposits are in the Oligocene part of the Lincoln Creek Formation, exposed along the Canyon and Satsop Rivers in western Washington. Each deposit preserves invertebrate fossils, many representing typical seep biota. Authigenic carbonates with δ13C values as low as −51‰ PDB reveal that the carbon is predominately methane derived. Carbonates contain the irregular isoprenoid hydrocarbons 2,6,11,15-tetramethylhexadecane (crocetane) and 2,6,10,15,19-pentamethylicosane (PMI), lipid biomarkers diagnostic for archaea. These lipids are strongly depleted in 13C (δ13C values as low as −120‰ PDB), indicating that archaea were involved in the anaerobic oxidation of methane. Small filaments preserved in the carbonate may represent methanotrophic archaea. Archaeal methanogenesis induced the formation of a late diagenetic phase, brownish calcite, consisting of dumbbell-shaped crystal aggregates that exhibit δ13C values as high as +7‰ PDB. Clotted microfabrics of primary origin point to microbial mediation of carbonate precipitation. Downward-directed carbonate aggregation in the seeps produced inverted stromatactoid cavities. Large filaments, interpreted as green algae based on their size, shape, arrangement and biomarkers, imply that deposition occurred, in places, in water no deeper than 210 m.