In this paper, we study uncertainty in estimating extreme floods of the Dongting Lake basin, China. We used three methods, including the Delta, profile likelihood function (PLF), and the Bayesian Markov chain Monte Carlo (MCMC) methods, to calculate confidence intervals of parameters of the generalized extreme value (GEV) distribution and quantiles of extreme floods. The annual maximum flow (AMF) data from four hydrologic stations were selected. Our results show that AMF data from Taoyuan and Xiangtan stations followed the Weibull class distribution, while the data from Shimen and Taojiang stations followed the Fréchet class distribution. The three methods show similar confidence intervals of design floods for short return periods. However, there are large differences between results of the Delta and the other two methods for long return periods. Both PLF and Bayesian MCMC methods have similar confidence intervals to reflect the uncertainty of design floods. However, because the PLF method is quite burdensome in computation, the Bayesian MCMC method is more suitable for practical use.