For the first time, a combination of metaheuristic algorithms and machine learning is used for hydrological drought analysis under climate change conditions and applications. The new framework is used by a novel hybrid machine learning model named the least-squares support vector machine-African vulture optimization algorithm (LSSVM-AVOA). The performance of the proposed hybrid algorithm was compared with three algorithms, including artificial neural network (ANN), adaptive neuro-fuzzy inference system (ANFIS), and least squares support vector machines (LSSVM). Using the technique for order of preference by similarity to the ideal solution (TOPSIS) method showed that LSSVM-AVOA with a score of 0.98 could be employed to improve the LSSVM modeling results. Three global climate models (GCM), including ACCESS-ESM1-5 (A1), CanESM5 (C5), and MRI-ESM2-0 (M2) during the historical period 1985–2014 and four scenarios, including SSP126, SSP245, SSP245-cov-fossil (SCF), SSP585 in future from 2021 to 2050 was considered for predicting discharge at Karun basin (Sepid Dasht Sezar, Bakhtiari Tang Pang, Sezar Tang Pang, Taleh Zang and Gotvand stations). Using new hybrid algorithm, the prediction results showed that discharge in most scenarios and stations decreased between − 0.81% and − 7.83% (except Sezar Tang Pang and Gotvand station). The standardized runoff index (SRI) results of hydrological drought analysis showed by the SSP585 scenario it seems that for the next first 10 years, a mild drought period can occur in this basin. Also, in the future period for SSP126 scenario by the first five years in the next 30 years, none drought is predicted.