Water deficit stress has become a significant challenge affecting agricultural production worldwide. The use of silicon (Si) and plant growth-promoting bacteria (PGPB) is known as an eco-friendly strategy to manage water deficit stress in agriculture. In this study, the combined effects of different rates and sources of Si (control, 100 mg nano-Si kg−1, 200 mg nano-Si kg−1, and 200 mg Si kg−1 from potassium silicate source) and native PGPB (no bacterium, Pseudomonas sp. 19, Bacillus sp. 76, and consortium of 19 and 76 strains) on morphophysiological and nutritional responses of canola and wheat were evaluated under water deficit stress. The results showed that the application of Si significantly enhanced the tolerance of canola and wheat to water deficit stress by increasing the shoot and root dry weights. On the other hand, Si and PGPB increased the concentration of N, P, K, and Si in canola and wheat shoots. Also, following the application of Si and PGPB, the content of malondialdehyde in canola and wheat decreased and the activity of superoxide dismutase, ascorbate peroxidase, and glutathione peroxidase also increased. The application of 100 mg nano-Si kg−1 and Pseudomonas sp. 19 resulted in the best performance in canola. However, the best results were achieved in wheat using 200 mg nano-Si kg−1 and Pseudomonas sp. 19. These results provided supporting evidence that the combined application of Si sources and PGPB optimally improved wheat and canola water deficit tolerance. The use of Si in combination with PGPB can be considered as an eco-friendly strategy for improving the tolerance of crop plants to drought stress in future.