Climate change has a significant impact on hydrological systems, particularly in vulnerable semi-arid regions like Algeria's Mekerra River basin. Since the 1970s, frequent droughts have reduced dam inputs, lowered groundwater levels, and depleted wells, underscoring the need for effective water resources management. This study aims to evaluate drought propagation in agricultural and hydrological systems, analyze drought trends, and assess climate change's hydrological impacts using drought indices, trend analysis, and hydrological modeling. Hydrometeorological data from 1980 to 2012 were used to calculate the Effective Reconnaissance Drought Index (eRDI) and the Standardized Streamflow Index (SSI) on 3- and 12-month scales, respectively, to assess drought propagation in agricultural and hydrological systems. Trend analysis was performed using the Improved Visualization of Innovative Trend Analysis (IV-ITA) to examine drought patterns via IV-ITA drought classification. The semi-distributed HBV-light model was applied to determine climate change's hydrological impact across upper, middle, and lower Mekerra sub-basins. The results indicate that the eRDI-3 revealed seasonal and spatial fluctuations in agricultural drought, with an extreme event in 1994 identified at Sidi Bel Abbes. The SSI-12 indicated significant flow variations between stations and reveal the longest and most extreme hydrological drought from 2002 to 2006. The IV-ITA indicated positive eRDI-3 trends at Hacaiba and Sidi Bel Abbes, non-monotonic trends elsewhere, while SSI-12 trends were negative at Sidi Ali Ben Youb, positive at Hacaiba, and non-monotonic at Sidi Bel Abbes. These trends clarified drought complexity in semi-arid contexts. The HBV-light model accurately reproduced the flow dynamics during calibration with acceptable validation performance for all the sub-basins, revealing low soil recharge that highlights drought's impact on water resources, particularly during the calibration period. These results provide robust methodologies and in-depth knowledge of the mechanisms of agricultural and hydrological drought in our semi-arid region and others similar, by enhancing trend assessment, supporting adaptive policies, and establishing early warning systems to strengthen resilience against climate change.