The analyses of radioactive isotopes 14C, 137Cs and 210Pb, and stable isotope 13C were performed in the sediment cores, top 40 cm, taken in 2011 from karst lakes Prošće and Kozjak in the Plitvice Lakes National Park, central Croatia. Frozen sediment cores were cut into 1 cm thick layers and dried. 14C activity in both carbonate and organic fractions was measured using accelerator mass spectrometry technique with graphite synthesis. 137Cs, 210Pb, 214Pb and 214Bi were measured by low level gamma spectrometry method on ORTECHPGe detector with the efficiency of 32%. Distribution of 14C activity from both lakes showed increase of the 14C activity in the top 10–12 cm in both carbonate and organic fractions as a response to thermonuclear bomb-produced 14C in the atmosphere in the sixties of the 20th century. Anthropogenically produced 137Cs was also observed in sediment profiles. Sedimentation rates for both lake sediments were estimated based on the unsupported 210Pb activity. Different 14C activity of the carbonate fraction (63–80 pMC, percent of modern carbon) and organic fraction (82–93 pMC) is the result of geochemical and biological processes of the sediment precipitation in the lake waters. This is also confirmed by the δ 13 C values of both fractions. Carbon isotope composition, a 14 C and δ 13 C, was compared with the lake sediments from the same lakes collected in 1989 and 2003.