Presented are results on the Pu and Th isotopes activity concentration found in the upper part of bottom sediments collected from a deep part of 29 lakes in N-E Poland by diving in 2000. Analyses of Pu isotopic ratios allowed for the discussion of Pu origin. Maximum percentage of 239+240Pu activity from Chernobyl fallout was 24%. Surface deposition of 239+240Pu was calculated. No relationship was found between the plutonium and main chemical matrix components of sample nor with the trophic status of the lake. Pu activities were weakly correlated with measured previously 137Cs activities.