Pomegranate cultivation has expanded significantly in the last two decades. However, there is limited information on its fertilization requirements and the effect of macronutrient availability on its reproductive development. Two commercial pomegranate cultivars—“Wonderful” and “Emek”—were grown in 500-L containers for 3 years, using a fertigation system. Development and reproduction indices were measured to explore the trees’ responses to elevated levels of nitrogen (N), phosphorus (P) and potassium (K) in the irrigation solution. Andromonoecy rate was affected by nutrient levels only in the first year of the experiment, with higher levels of N and P leading to a greater proportion of hermaphrodites out of total flowers. P level had a positive effect on the total number of hermaphrodites per tree in both varieties. Differences recorded between hermaphroditic and staminate flowers included nutrient concentrations and dry weight. Fruit set and aril number were positively affected by N concentration in the irrigation solution. We conclude that only a severe deficiency of N and P affects the andromonoecy trait, and that at the levels examined in this study, K hardly influences pomegranate reproduction.