Methane seep deposits, comprising large, carbonate-rich mounds formed from hydrocarbon seepage, were widely distributed in the Late Cretaceous Western Interior Seaway (WIS) of North America. Well-preserved, methane-derived authigenic carbonates (MDACs) from these deposits have been shown to retain petrological, paleontological, and geochemical imprints of their ancient depositional setting, all of which are important for understanding the dynamics and evolution of the shallow, epeiric WIS. To better characterize the environmental conditions of WIS seeps, we applied clumped isotope paleothermometry to magnesium calcite MDAC samples from five seep localities in the upper Campanian Pierre Shale, South Dakota, USA. We measured 21 subsamples, including 18 micritic carbonates and demonstrated apparent clumped isotope equilibrium between MDACs and WIS bottom waters. Extreme ¹³C depletion in most samples (δ¹³C ranging to −45.44‰) indicates they were precipitated with oxidized methane as a major source of dissolved inorganic carbon, which itself implies a close association with ancient methanotrophic metabolism. The average clumped isotope paleotemperature from the micritic carbonates is 23 ± 7 °C (1σ standard deviation), which agrees with bottom water paleotemperatures inferred from δ¹⁸O measurements of MDACs and well-preserved mollusk shells at similar localities in the WIS. The calculated average δ¹⁸O_w value for these samples is −0.5 ± 1.7‰ (1σ SD), which is indistinguishable from previously reported calculation on Campanian seawater δ¹⁸O_w from fossil mollusk shells, but elevated above younger fossils collected from other locations in the WIS. Our conclusions are inconsistent with previously hypothesized disequilibrium for WIS MDAC clumped isotope and therefore we propose that fossil MDAC deposits may be used as paleotemperature archives.