Water productivity (WP) of crops is affected by water–fertilizer management in interaction with climatic factors. This study aimed to evaluate the efficiency of a hybrid method of season optimization algorithm (SO) and support vector regression (SVR) in estimating the yield and WP of tomato crops based on climatic factors, irrigation–fertilizer under the drip irrigation, and plastic mulch. To approve the proposed method, 160 field data including water consumption during the growing season, fertilizers, climatic variables, and crop variety were applied. Two types of treatments, namely drip irrigation (DI) and drip irrigation with plastic mulch (PMDI), were considered. Seven different input combinations were used to estimate yield and WP. R2, RMSE, NSE, SI, and σ criteria were utilized to assess the proposed hybrid method. A good agreement was presented between the observed (field monitoring data) and estimated (calculated with SO–SVR method) values (R2 = 0.982). The irrigation–-fertilizer parameters (PMDI, F) and crop variety (V) are the most effective in estimating the yield and WP of tomato crops. Statistical analysis of the obtained results showed that the SO–SVR hybrid method has high efficiency in estimating WP and yield. In general, intelligent hybrid methods can enable the optimal and economical use of water and fertilizer resources.