Results for, Cs-137, Pu and Th isotopes activity concentration found in the upper part of bottom sediments taken from a deep part of 29 lakes on Mazurian Lakes area (North-Eastern Poland). Samples were collected by diving. Results for 137Cs were obtained using low background gamma ray spectrometry, Pu-238, Pu-239+240, Th-230 and Th-232 were obtained by means of alpha spectrometry and those for 241Pu were obtained using liquid scintillation spectrometry. Activities for Pu-239+240 range from 81(13) mBq/kg to 3820(265) mBq/kg, whereas for Pu-238 they range from 9(5) mBq/kg up to 549(122) mBq/kg. Arithmetic mean activity for Pu-239+240 was 1285 mBq/kg with the standard deviation equal to 1012 mBq/kg. Analyses of Pu isotopic ratios allowed for the discussion of Pu origin. Maximum percentage of Pu-239+240 activity from Chernobyl fallout was 24%. It was significantly lower then found in previous measurements in forests at the same region of Poland. It suggest a difference in Chernobyl hot particles fallout between forests and lakes. Surface deposition of Pu-239+240 was calculated. No clear relationship was found between the plutonium and main chemical matrix components of sample nor with the trophic status of the lake. Pu activities were not well correlated with measured Cs-137 activities. Pu activities were not correlated with Th activities. Th-230 and Th-232 were strongly correlated.