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With the intensification of climate change, its impact on runoff variations cannot be ignored. The main purpose of this study is to analyse the nonstationarity of runoff frequency adjusted for future climate change in the Luanhe River basin, China, and quantify the different sources of uncertainties in nonstationary runoff frequency analysis. The advantage of our method is the combination of generalized additive models in location, scale, and shape (GAMLSS) and downscaling models. The nonstationary GAMLSS models were established for the nonstationary frequency analysis of runoff (1961-2010) by using the observed precipitation as a covariate, which is closely related to runoff and contributes significantly to its nonstationarity. To consider the nonstationary effects of future climate change on future runoff variations, the downscaled precipitation series in the future (2011-2080) from the general circulation models (GCMs) were substituted into the selected nonstationary model to calculate the statistical parameters and runoff frequency in the future. A variance decomposition method was applied to quantify the impacts of different sources of uncertainty on the nonstationary runoff frequency analysis. The results show that the impacts of uncertainty in the GCMs, scenarios, and statistical parameters of the GAMLSS model increase with increasing runoff magnitude. In addition, GCMs and GAMLSS model parameters have the main impacts on runoff uncertainty, accounting for 14% and 83% of the total uncertainty sources, respectively. Conversely, the interactions and scenarios make limited contributions, accounting for 2% and 1%, respectively. Further analysis shows that the sources of uncertainty in the statistical parameters of the nonstationary model mainly result from the fluctuations in the precipitation sequence. This result indicates the necessity of considering the precipitation sequence as a covariate for runoff frequency analysis in the future.