Lake Taihu, the third largest freshwater lake in China, suffers from harmful cyanobacteria blooms caused by Microcystis spp., which do not fix nitrogen (N). Reduced N (i.e., NH₄⁺, urea and other labile organic N compounds) is an important factor affecting the growth of Microcystis. As the world use of urea as fertilizer has escalated during the past decades, an understanding of how urea cycling relates to blooms of Microcystis is critical to predicting, controlling and alleviating the problem. In this study, the cycling rates of urea-N in Lake Taihu ranged from non-detectable to 1.37 μmol N L⁻¹ h⁻¹ for regeneration, and from 0.042 μmol N L⁻¹ h⁻¹ to 2.27 μmol N L⁻¹ h⁻¹ for potential urea-N removal. The fate of urea-N differed between light and dark incubations. Increased ¹⁵NH₄⁺ accumulated and higher quantities of the removed urea-¹⁵N remained in the ¹⁵NH₄⁺ form were detected in the dark than in the light. A follow-up incubation experiment with ¹⁵N-urea confirmed that Microcystis can grow on urea but its effects on urea dynamics were minor, indicating that Microcystis was not the major factor causing the observed fates of urea under different light conditions in Lake Taihu. Bacterial community composition and predicted functional gene data suggested that heterotrophic bacteria metabolized urea, even though Microcystis spp. was the dominant bloom organism.