Plastics have been produced for over a century, but definitive evidence of complete plastic biodegradation in different habitats, particularly freshwater ecosystems, is still missing. Using 13C-labeled polyethylene microplastics (PE-MP) and stable isotope analysis of produced gas and microbial membrane lipids, we determined the biodegradation rate and fate of carbon in PE-MP in different freshwater types. The biodegradation rate in the humic-lake waters was much higher (0.45±0.21% per year) than in the clear-lake waters (0.07±0.06% per year) or the artificial freshwater medium (0.02±0.02% per year). Complete biodegradation of PE-MP was calculated to last 100-200 years in humic-lake waters, 300-4000 years in clear-lake waters, and 2000-20000 years in the artificial freshwater medium. The concentration of 18:1ω7, characteristic phospholipid fatty acid in Alpha- and Gammaproteobacteria, was a predictor of faster biodegradation of PE. Uncultured Acetobacterioceae and Comamonadacea among Alpha- and Gammaproteobacteria, respectively, were major bacteria related to the biodegradation of PE-MP. Altogether, it seems that microbes in the humic lakes with natural refractory polymers have a better ability to decompose PE than in other waters.