This dataset describes six sediment cores (12 - 219 cm length) from different landscape features in a coastal permafrost thermokarst affected landscape in the Theshekpuk Lake region in Arctic Alaska. They are located in a transect from inland to coast, to describes the transitional dynamics between terrestrial and marine permafrost and thermokarst. The cores were drilled during the Perma-X Lagoon expedition in April 2022. The three unfrozen cores from a marine (MAR, 12 cm length), an intact lagoon (LAG, 31 cm length) and a thermokarst lake (TKL, 50 cm length) site, were all sampled using a Push Corer. The three frozen cores, including upland permafrost (UPL, 203 cm length), drained thermokarst lake basin (DLB, 219 cm length) and semi-drained lagoon (SDLAG, 183 cm length) deposits, were drilled using a SIPRE Corer. For the lipid-biomarker analysis 15 subsamples were selected. In case of the shortest core (MAR) only one sample, in case of the medium length unfrozen cores (LAG, TKL) two samples and in case of the frozen cores three, respectively four samples in case of the longest core from the DLB, were selected. The measured parameters and calculated indices included the total concentration of n-alkanes [µg/gTOC], the total concentration of n-alkanols [µg/gTOC], Average chain length (ACL), Paq, Pwax, carbon preference index (CPI), and higher plant index (HPA). The data is related to the paper Organic Carbon, Mercury, and Sediment Characteristics along a land – shore transect in Arctic Alaska , Giest et al. (currently in submission).