Study of ancient cold-methane seep deposits provides insight into the changes in seep communities over the lifetime of a seep, which are otherwise difficult to observe in modern settings. We studied 24 cold-methane seep deposits in the Upper Cretaceous (Campanian) Pierre Shale of southwestern South Dakota. These deposits were subdivided into three categories depending on their physical characteristics: (1) those with a single main conduit, few secondary pipes and concretionary bodies, and no carbonate cap, implying strong advective flow to the sediment-water interface; (2) those with a single main conduit, a moderate number of secondary pipes and concretionary bodies, and a small carbonate cap, implying both advective and diffusive flow to the sediment-water interface; and (3) those with a single main conduit, a high number of secondary pipes and concretionary bodies, and a broad carbonate cap, implying extensive flow, but dampening at the sediment-water interface due to the presence of the large carbonate cap. We analyzed the faunal composition at all 24 seeps. The number of species ranges from five to 20. All of the seeps are dominated by baculitid ammonites, inoceramids, and lucinids (“foundation” organisms). These species are the same as those in time-equivalent non-seep sites in the Pierre Shale and are not seep-obligate. However, in seep categories 2 and 3, the number and kind of secondary organisms increases in association with the development of the large carbonate cap. These organisms include oysters, gastropods, echinoids, sponges, crinoids, and scaphitid ammonites. We infer that these organisms appear because (1) the carbonate hardground provides a more diverse habitat allowing attachment and encrustation and (2) the bottom waters are better oxygenated and/or the level of hydrogen sulfide is reduced because the methane rich fluids are diverted away from the carbonate cap, thus providing a more suitable habitat for organisms such as scaphitid ammonites that require a well-oxygenated environment. However, even at these seeps, the number of secondary organisms usually does not exceed that of foundation organisms.