This dataset presents an estimation of the organic matter content (by loss-on-ignition) and particle size (grain size analysis) in two lake sediment cores (109 cm, 114 cm) from two different lakes located on Bylot Island, Nunavut, Canada. The cores were collected in June 2015 at « Gull Lake » (also named BYL-66 in other publications) and lake K (also named BYL-36) from the still-present ice cover with a 7 cm-diameter percussion corer (Aquatic Research Instruments). First, samples were collected at each cm along the cores, then freeze-dried and combusted (550 °C for 4 h) to remove the organic fraction. Second, a part of these samples was grouped into stratigraphic sub-units based on visual descriptions of the core. These samples were analyzed for their grain size distribution, either by sieving for coarser material (sand, gravel), or by hydrometry for finer sediment (clay, silt). For lake K, the finer fraction of the subsamples were analyzed by laser diffraction.