Early growth water stress reduces the extract and fresh oil of Silybum marianum L. (S. marianum) shoots. Two experiments were conducted to reduce the effects of early growth drought. Treatments in the first experiment were organic seed cover fillers at three levels (control, vermicompost, and peat moss), hydrogel at seven levels (control, 2, 4, and 6 g hydrogelF1 per kg OSC, and 2, 4, and 6 g hydrogelA200 per kg organic seed cover), and water deficit at three levels (100, 50, and 25% of field capacity), and in the second experiment, seeds were inoculated with bacteria at four levels (control, Pseudomonas fluorescens, Pseudomonas putida, and their combination) and water deficit at four levels (100, 50, and 25% of field capacity). Our results showed that milk thistle seeds are sensitive to water deficit at the emergence stage. Covering milk thistle (S. marianum) seeds with organic seed cover increased water retention around the seeds and improved emergence percentage. Use of organic seed cover with hydrogel increased relative water content (RWC), leaf area, and shoot length, and increased extracts and oils in fresh shoots. Bacterial inoculation also improved initial growth and reduced the effect of water stress on the plant, and increased leaf number, extract, and oil. The combination of bacteria had a positive effect on initial growth and inoculation of seeds, P. fluorescens and P. putida increased relative water content (RWC), shoot height, and specific leaf area, and increased extract and oil under water deficit conditions. A comparison of the results showed that seed inoculation is a simple method without new culture medium, and improves extract and oil under water deficit conditions.