Improving reference evapotranspiration (RET) estimation accuracy contributes to effective water resource management, irrigation planning, and climate change assessments in agricultural systems. The widely recommended FAO-56 Penman-Monteith (PM-FAO56) model for RET estimation often faces limitations due to incomplete meteorological data availability. To address this, we evaluate the ability of eight empirical models, four machine learning (ML) models and their hybrid models to estimate daily RET in Gharb and Loukkos irrigated perimeters in Morocco. These ML and hybrid models include Random Forest (RF), M5 Pruned (M5P), eXtreme Gradient Boosting (XGBoost), Light Gradient Boosting Machine (LightGBM), RF-M5P, RF-XGBoost, RF-LightGBM and XGBoost-LightGBM. Additionally, six input combinations (based on Tmax, Tmin, RHmean, Rs and U2) were designed, with PM-FAO56 model considered as a target to models. Four statistical indicators including Kling Gupta Efficiency index (KGE), Coefficient of determination (R2), Mean Squared Error (RMSE), and Root relative squared error (RRSE) were applied to assess the models’ performance, across both training and testing phases. The findings reveal that Valiantzas 2013 (VAL2013b) model outperformed the other empirical models for all station, exhibiting high KGE and R2 (0.95–0.97), low RMSE (0.32–0.35 mm.day-1) and RRSE (8.14–10.30%). Additionally, the Hargreaves and Samani 1985 (HargS1985) model performed well in Gharb's stations, while the Valiantzas 2013 (VAL2013a) model showed good results in Loukkos' stations. Besides, the ML model’s performance RET estimation was higher when Tmax, Tmin, RHmean, Rs and U2 were used as inputs (combination 6). Among the ML and hybrid models, the XGBoost-LightGBM and RF-LightGBM achieved the highest accuracy (on average RMSE 0.015–0.097 mm.day-1), closely followed by the LightGBM and XGBoost models. However, M5P model had the lowest estimation accuracy RMSE ranged from 0.022 to 0.108 mm.day-1 on average. In summary, our study highlights the potential of ML models for RET estimation in subhumid and semi-arid areas, providing vital insights for improving water resource management, helping climate change research and optimizing irrigation scheduling for optimal agricultural water usage in the region.