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Abstract Ancient greenhouse periods are useful analogs for predicting effects of anthropogenic climate change on regional and global temperature and precipitation patterns. A paucity of terrestrial data from polar regions during warm episodes challenges our understanding of polar climate responses to natural/anthropogenic change and therefore our ability to predict future changes in precipitation. Ellesmere and Axel Heiberg Islands in the Canadian Arctic preserve terrestrial deposits spanning the late Paleocene to middle Eocene (59–45 Ma). Here we expand on existing regional sedimentology and paleontology through the addition of stable (δ¹³C, δ¹⁸O) and clumped (Δ₄₇) isotope analyses on palustrine carbonates. δ¹³C isotope values range from −4.6 to +12.3‰ (VPDB), and δ¹⁸O isotope values range from −23.1 to −15.2‰ (VPDB). Both carbon and oxygen isotope averages decrease with increasing diagenetic alteration. Unusually enriched carbon isotope (δ¹³C) values suggest that analyzed carbonates experienced repeated dissolution‐precipitation enrichment cycles, potentially caused by seasonal fluctuations in water availability resulting in summer carbonate dissolution followed by winter carbonate re‐precipitation. Stable isotopes suggest some degree of precipitation seasonality or reduction in winter water availability in the Canadian Arctic during the Paleogene. Clumped (Δ₄₇) temperature estimates range from 52 to 121°C and indicate low temperature solid‐state reordering of micritic samples and diagenetic recrystallization in sparry samples. Average temperatures agree with vitrinite reflectance data for Eureka Sound Group and underlying sediments, highlighting structural complexity across the region. Broadly, combined stable and clumped isotope data from carbonates in complex systems are effective for describing both paleoclimatic and post‐burial conditions.