Resource management and climate resilience depend on an understanding of hydroclimatic variability in the Sahel and Sudan. This study uses meteorological data, drought indices (SPI, SPEI), and trend detection techniques to compare drought dynamics in two agroecological locations in Mali, Cinzana (Sahelian zone) and Kola (Sudanian zone), from 1994 to 2022. The results show different trajectories: Kola shows significant warming, particularly in minimum temperatures, with a 2008 breakpoint indicating accelerated nighttime warming, while Cinzana shows no significant rainfall or temperature trends but a positive SPEI-12 signal consistent with Sahelian “regreening.” At Kola, negative trends in SPI-12, SPEI-6, and SPEI-9 indicate worsening aridification. Rainfall is the main cause of drought variability at multi-annual ranges, according to correlation analysis, with evapotranspiration becoming more important at seasonal periods. These results highlight the coexistence of drying and greening over short distances, underscoring the necessity of fine-scale evaluations to enhance regional climate projections and direct distinct adaptation measures for agriculture and water.