This study was conducted to investigate the effects of various irrigation water (W) and nitrogen (N) levels on growth, root-shoot morphology, yield, and irrigation water use efficiency of greenhouse tomatoes in spring–summer and fall–winter. The experiment consisted of three irrigation water levels (W: 100% of crop evapotranspiration (ETc), 80%, and 60% of full irrigation) and three N application levels (N: 100%, 75%, and 50% of the standard nitrogen concentration in Hoagland’s solution treatments equivalent to 15, 11.25, 7.5 mM). All the growth parameters of tomato significantly decreased (p < 0.05) with the decrease in the amount of irrigation and nitrogen application. Results depicted that a slight decrease in irrigation and an increase in N supply improved average root diameter, total root length, and root surface area, while the interaction was observed non-significant at average diameter of roots. Compared to the control, W₈₀ N₁₀₀ was statistically non-significant in photosynthesis and stomatal conductance. The W₈₀ N₁₀₀ resulted in a yield decrease of 2.90% and 8.75% but increased irrigation water use efficiency (IWUE) by 21.40% and 14.06%. Among interactions, the reduction in a single factor at W₈₀ N₁₀₀ and W₁₀₀ N₇₅ compensated the growth and yield. Hence, W₈₀ N₁₀₀ was found to be optimal regarding yield and IWUE, with 80% of irrigation water and 15 mM of N fertilization for soilless tomato production in greenhouses.