Algae and macrophytes in lake ecosystems regulate nitrous oxide (N2O) emissions from eutrophic lakes. However, knowledge of diurnal N2O emission patterns from different habitats remains limited. To understand the diurnal patterns and driving mechanisms of N2O emissions from contrasting habitats, continuous in situ observations (72 h) of N2O fluxes from an algae-dominated zone (ADZ) and reed-dominated zone (RDZ) in Lake Taihu were conducted using the Floating Chamber method. The results showed average N2O emission fluxes of 0.15 ± 0.06 and 0.02 ± 0.04 μmol m−2 h−1 in the ADZ and RDZ in autumn, respectively. The significantly higher (p < 0.05) N2O fluxes in the ADZ were mainly attributed to differences in nitrogen (N) levels. The results also showed significant diurnal differences (p < 0.05) in the N2O emission fluxes within the ADZ and RDZ, and daytime fluxes were significantly higher (p < 0.05) than nighttime fluxes. The statistical results indicated that N2O emissions from the ADZ were mainly driven by diurnal variations in N loading and the dissolved oxygen (DO) concentration, and those from the RDZ were more influenced by DO, redox potential, and pH. Finally, we determined the proper time for routine monitoring of N2O flux in the two habitats. Our results highlight the importance of considering diverse habitats and diurnal variations when estimating N2O budgets at a whole-lake scale.