In Mali, the annual temperature, rainfall, and evapotranspiration are high variables. Their distributions are unevenly spread from north to south. Climate change strengthens to increase air temperature and evapotranspiration. It also increases the intense rainstorms and the risk of drought associated heat waves. Drought is considered a natural disaster among all hydrologic extremes. It causes severe damage to the environment, agriculture, and livelihoods relying on water resources. The present study evaluated the variation of drought indices from 1989 to 2019 in Koutiala and San districts, respectively. Therefore, the Standardized Precipitation Evapotranspiration Index (SPEI) was applied. Hence, the Mann-Kendall (MK) test was used and for 12-month time-scales. Trend analysis of monthly precipitation, temperature, and evapotranspiration has been done by using the MK test. Based on the analysis result, the climate of the Koutiala and San districts has been classified as moderate to severe drought category. However, this result clearly shows SPEI pattern changes in both districts. The monthly precipitation showed a significant decreasing trend in Koutiala and San districts. In comparison, the monthly temperature and evapotranspiration displayed an increasing trend in both districts.