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Recent climate change studies have given a lot of attention to the uncertainty that stems from general circulation models (GCM), greenhouse gas emission scenarios, hydrological models and downscaling approaches. Yet, the uncertainty that stems from the selection of the baseline period has not been studied. Accordingly, the main research question is as follows: What would be the differences and/or the similarities in the evaluation of climate change impacts between the GCM and the delta perturbation scenarios using different baseline periods? This article addresses this issue through comparison of the results of two different baseline periods, investigating the uncertainties in evaluating climate change impact on the hydrological characteristics of arid regions. The Lower Zab River Basin (Northern Iraq) has been selected as a representative case study. The research outcomes show that the considered baseline periods suggest increases and decreases in the temperature and precipitation (P), respectively, over the 2020, 2050 and 2080 periods. The two climatic scenarios are likely to lead to similar reductions in the reservoir mean monthly flows, and subsequently, their maximum discharge is approximately identical. The predicted reduction in the inflow for the 2080-2099 time period fluctuates between 31 and 49% based on SRA1B and SRA2 scenarios, respectively. The delta perturbation scenario permits the sensitivity of the climatic models to be clearly determined compared to the GCM. The former allows for a wide variety of likely climate change scenarios at the regional level and are easier to generate and apply so that they could complement the latter.