Vachellia nilotica and Bombax ceiba are multipurpose tree species being used in different agroforestry systems and irrigated forest plantations. Both are commonly used as source of tannin, gum, timber, medicine, and fuelwood etc. Scarcity of water and low soil fertility are major problems in arid to semiarid regions of Pakistan, resulting in reduced crop and forest yield. It can be rectified by applying optimal doses of organic and inorganic fertilizers with best irrigation levels. The effect of farmyard manure (FYM), nitrogen, phosphorus and potassium (NPK) fertilizers along with irrigation levels were compared on the seedling growth V. nilotica and B. ceiba at the research station of Department of Forestry and Range Management, University of Agriculture Faisalabad, Pakistan. Different doses of NPK and FYM (T0 = Control, T1 = NPK2, T2 = NPK1, T3 = NPK2+ FYM2, T4 = NPK2+ FYM1, T5 = NPK1+ FYM2, T6 = NPK1+ FYM1) were applied with two irrigation levels, and water was applied at fixed intervals i.e., 7 and 14 days. It was concluded that maximum growth response of morphological (height, diameter, shoot fresh weight, root fresh weight, shoot dry weight, root dry weight, total biomass, moisture content availability) and physiological parameters (transpiration rate, photosynthetic rate, stomatal conductance) were recorded at T6 (maximum irrigation and fertilizer levels), with 7 days irrigation interval and minimum response was recorded at T0 (minimum irrigation and fertilizer levels). Furthermore, the findings of study highlighted the necessity of organic and inorganic fertilizers in improving the biomass of tree species for reducing the rotation age in agroforestry systems.