Core sediment (sapropel) samples were collected from Lake Okunozero, the Republic of Karelia, Russia, to assess the distribution of heavy metals and their main fractions, probable sources of pollution, and potential ecological and toxicological risks for the water body. Heavy metal concentrations were measured by the mass spectrometry method using an XSeries-2 ICP-MS. The sequential extraction of heavy metals from sapropel samples was performed using the scheme of Tessier. According to the Russian Interstate Standard (GOST), the sapropel of Lake Okunozero is suitable for use in agriculture. The exceedances of the regional background levels were detected only for Pb and Cd. In accordance with Pollution Load Index (PLI) and Potential Ecological Risk (RI), no ecotoxicological risk in researched sediments was found. A significant correlation between some investigated heavy metals was established. Most heavy metals were in the insoluble mineral phase (Mn et al.) or were associated with organic matter (Cu, Zn, Mo, Ni). Only Mn, Zn, Cd, and Pb were found in the available fraction from 13 to 24% of the total metal content in the sediments. Other metals were less associated with the available fraction.