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Arid pomegranate (Punta granatum) orchards are frequently rainfed. In these systems, orchard managers might be able to manipulate a stand’s canopy structure (e.g., thinning, pruning) to improve rainfall water input to the soil. The aim of this research was to determine how changes in management activities in rainfed pomegranate orchards in arid regions of Central Iran affects rainfall partitioning into throughfall, stemflow, and rainfall interception loss. We monitored gross rainfall, throughfall, stemflow and rainfall interception loss in three stands with varying levels of thinning and pruning. Management practices sufficiently altered the stand and canopy structure of pomegranate orchards to impact the quantity and pathway (throughfall v. stemflow) of rainfall reaching the ground. Decreases in tree height, canopy cover, crown length and LAI were correlated to a significant increase in rainfall reaching the forest floor. Results indicate that orchard managers may be able to prune 40% of the live crown and thin 70% of the stand if the objective it to significantly increase water inputs into the soil. Future research should focus on the impact of canopy management on soil moisture content and soil evaporation and transpiration.