This study presents results of research on the number of heterotrophic bacteria and fungi in water and bottom sediments of Lake Chełmżyńskie and their role in the decomposition of chitin. The authors also examined the level of respiration activity of water and sediment microorganisms in the presence of shrimp waste. Results demonstrate that the number of heterotrophic bacteria and fungi in water and bottom sediments were variable. The analyzed groups of microorganisms predominated in bottom sediments with the number of heterotrophic bacteria significantly exceeding that of fungi. The proportion of microorganisms capable of decomposing chitin was greater among fungi than among heterotrophic bacteria. In water chitinolytic bacteria constituted 11–19% of the total number of heterotrophic bacteria and in bottom sediments only 3–8%. Chitinolytic fungi constituted 17–67% and dominated in water. In the presence of shrimp waste, the level of respiration activity of microorganisms in water and bottom sediments of Lake Chełmżyńskie clearly depended on examined factors. The temperature, incubation time, and type of respiration substrate had a statistically significant impact on this activity. The highest respiration activity (2.4–90.3 mg O₂ · dm^-3) of aquatic microorganisms was recorded in the summer, when the water temperature equaled 24°C. In bottom sediments the highest values of respiration activity also were observed in summer (13.4–447.4 mg O₂ g^-1dry mass) but alkaline sediments were characterized by higher activity levels. Benthic and planktonic microorganisms were utilizing shrimp heads most effectively and the exoskeletons least effectively.