The root zone soil moisture (RZSM) is essential for monitoring and forecasting agricultural, hydrological, and meteorological systems. Accordingly, researchers are determined to improve robust machine learning (ML) models to increase the accuracy of the RZSM predictions. This paper designed new complementary forecasting paradigms hybridizing Empirical Wavelet Transform (EWT) and two modern ensemble-based ML models, namely, extreme gradient boosting (XGBoost) and categorical boosting (CatBoost), to forecast long-term multi-step ahead daily RZSM in very cold and very warm semi-arid regions of Iran. For this purpose, the required datasets consisting of soil properties and meteorological information were extracted from the satellite datasets during 2005–2020 for Ardabil and Minab sites. Afterward, the significant lags of RZSM time series and optimal influence candidate inputs were sought based on the partial autocorrelation function (PACF) and mutual information techniques, respectively. Selected lagged components of RZSM time series were decomposed using EWT into different sub-sequences and consequently concatenated with candidate inputs to feed the ensemble ML models to forecast one-, three-, and seven-day-ahead RZSM at each case study. The performance of EWT-CatBoost and EWT-XGBoost and their counterpart standalone approaches was firstly evaluated in forecasting one-, three-, and seven-day-ahead RZSM using satellite data in this study and their accuracy were compared with a standalone kernel ridge regression (KRR) and complementary EWT-KRR models based on several statistical metrics (e.g., correlation coefficient (R), root mean square error (RMSE), Nash–Sutcliffe model efficiency coefficient (NSE)) and diagnostic analysis. The outcomes of testing phase in Ardabil site ascertained that the EWT-CatBoost (for RZSM(t + 1), R= 0.9979, RMSE= 0.0019, and NSE= 0.9985; for RZSM(t + 3), R= 0.9934, RMSE= 0.0035, and NSE= 0.9885; for RZSM(t + 7), R= 0.9489, RMSE= 0.0109, and NSE= 0.8634) outperformed the other models. On the other hand, the EWT-XGBoost model according to its best results (for RZSM(t + 1), R= 0.9911, RMSE= 0.0064, and NSE= 0.9805; for RZSM(t + 3), R= 0.9807, RMSE= 0.0092, and NSE= 0.9589; for RZSM(t + 7), R= 0.9680, RMSE= 0.0120, and NSE= 0.9309) yielded the most promising accuracy in forecasting multi-step ahead daily RZSM followed by the EWT-CatBoost, and EWT-KRR, respectively.