Revealing the mechanism of hydrological and agricultural drought has been challenging and vital in the environment under extreme weather and water resource shortages. To explore the evolution process from meteorological to hydrological and agricultural drought further, multi-source remote sensing data, including the Gravity Recovery and Climate Experiment (GRACE) product, were collected in the Huaihe River basin of China during 2002–2020. Three machine learning methods, including long short-term memory neural network (LSTM), convolutional neural network (CNN), and categorical boosting (CatBoost), were constructed for hydrological and agricultural drought forecasting. The propagation time from meteorological drought to surface water storage and terrestrial water storage drought, evaluated by the standardized precipitation evapotranspiration index, was 8 and 11 months with Pearson correlation coefficients (R) of 0.68 and 0.48, respectively. Groundwater storage drought was correlated with evapotranspiration and vegetation growth with a 12-month lag time, respectively. In addition, vegetation growth was affected by the drought of soil moisture at depths ranging from 100 to 200 cm with an 8-month lag time with an R of −0.39. Although the forecasting performances of terrestrial water storage drought were better than those of groundwater storage drought and agricultural drought, CNN always performed better than LSTM and CatBoost models, with Nash–Sutclife efficiency values during testing ranging from 0.28 to 0.70, 0.26 to 0.33, and −0.10 to −0.40 for terrestrial water storage drought, groundwater storage drought, and agricultural drought at lead times of 0–3 months, respectively. Furthermore, splitting training and testing data at random significantly improved the performances of CNN and CatBoost methods for drought forecasting rather than in chronological order splitting for non-stationary data.