The data set includes the results of geochemical and sediment analyses on 7 sediment cores (63.2 cm - 86.5 cm) from two northern Alaskan thermokarst lakes (Emaiksoun and Unnamed Lake). The analysis include lake depth measurements, linescan imaging, XRF scans, grainsize distribution, loss on ignition, porewater content, magnetic susceptibility, dissolved organic carbon concentration, sediment density, stable carbon isotope measurements dissolved organic carbon and soil organic carbon and radiocarbon ages.