Stationarity is often assumed for frequency analysis of low flows in water resources management and planning. However, many studies have shown that flow characteristics, particularly the frequency spectrum of extreme hydrologic events, were modified by climate change and human activities. Thus, the conventional frequency analysis that fails to consider the nonstationary characteristics may lead to costly design. The analysis presented in this paper was based on the more than 100 years of daily flow data from the Yichang gauging station 44 km downstream of the Three Gorges Dam. The Mann–Kendall trend test under the scaling hypothesis showed that the annual low flows had a significant monotonic trend, whereas an abrupt change point was identified in 1936 by the Pettitt test. The climate-informed low-flow frequency analysis and the divided and combined method were employed to account for the impacts from related climate variables and nonstationarities in annual low flows. Without prior knowledge of the probability density function for the gauging station, six distribution functions including the generalized extreme values (GEV), Pearson Type III, Gumbel, Gamma, Lognormal and Weibull distributions have been tested to find the best fit, in which the local likelihood method is used to estimate the parameters. Analyses show that GEV had the best fit for the observed low flows. This study has also shown that the climate-informed low-flow frequency analysis is able to exploit the link between climate indices and low flows, which would account for the dynamic feature for reservoir management and provide more accurate and reliable designs for infrastructure and water supply. Copyright © 2014 John Wiley & Sons, Ltd.