The vertical distribution of radiocarbon (14C) was examined in the bottom sediment core, taken from Lake Drūkšiai, which has served as a cooling pond since 1983 for the 26 years of the Ignalina Nuclear Power Plant (INPP) operation using two RBMK-1500 reactors (Russian acronym for”Channelized Large Power Reactor”). 14C specific activity was measured in alkali-soluble and -insoluble fractions of the sediment layers. Complementary measurements of the 210Pb and 137Cs activity of the samples provided the possibility to evaluate the date of every layer formation, covering the 1947–2013 period. In addition, 14C distribution was examined in the scales of pelagic fish caught between 1980 and 2012. Our measurements reveal that, during the period 1947–1999, the radiocarbon specific activity in both fractions exhibits a parallel course with a difference of 5 ± 1 pMC (percent of modern carbon) being higher in alkali-soluble fraction, although 14C specific activity in both fractions increased by 11.4–13.6 pMC during the first 15 years of plant operation. However, during the 2000–2009 period, other than previously seen, a dissolved inorganic carbon (DIC) → aquatic primary producers → sediments 14C incorporation pattern occurred, as the radiocarbon specific activity difference between alkali-soluble and -insoluble fractions reached 94, 25, and 20 pMC in 2000, 2006, and 2008, respectively. Measurements in different sediment fractions allowed us to identify the unexpected organic nature of 14C contained in liquid effluences from the INPP in 2000–2009. The discrepancy between 14C specific activity in fish scales samples and DIC after 2000 also confirmed the possibility of organic 14C contamination. Possible reasons for this phenomenon might be industrial processes introduced at the INPP, such as the start of operation of the cementation facility for spent ion exchange resins, decontamination procedures, and various maintenance activities of reactor aging systems and equipment.