Biota living in lakes and their watersheds are the sources of organic compounds for lake sediments. Much of the organic matter contained in sediments has undergone microbial reprocessing. Nevertheless, organic matter in lake sediments can retain source information and thereby contribute to the paleolimnological record. In sediment cores from Mansar and Surinsar lakes of Lesser Himalaya, Jammu, C/N ratios and ¹³C values suggest that the primary source of organic carbon was vascular land plants. Low total nitrogen contents, low amino acid/amino sugar ratios, low amino acid carbon and nitrogen contents, and low ¹⁵N values, the latter in Mansar lake, suggest terrigenous organic matter higher in lignin or carbohydrate contents and biodegradation in bottom sediments. The higher ¹⁵N values in Surinsar lake indicates more autochthonous contribution of organic content. Variations in the organic carbon and total nitrogen contents in the cores are related to grain size, inorganic carbonate, and degradation at the bottom levels. The ²¹⁰Pb data of the core fractions of these lakes show variation in the rate of sedimentation in Mansar lake, that is, 8.2 mm/yr in the northern and 4.5 mm/yr in the southern flank, whereas in Surinsar lake, it is 7.2 mm/yr, which indicates variation in sedimentation/erosion in the lake basins.