Organic amendments are used to improve unsuitable or disturbed physical and chemical properties of soils. In this study, the effects of long-term (1996-2008) manure, compost and mycorrhiza-use on saturated hydraulic conductivity and nitrate (NO3-N) leaching in clay-loamy soils of Cukurova region located in Eastern Mediterranean were investigated. The study consisted of control, mineral fertilizing (300-60-150 kg N-P-K ha(-1)), manure (25 tons ha(-1)). compost (25 tons ha(-1)) and mycorrhiza-inoculated compost (10 tons ha(-1)) with three replicates. The effects of long-term mycorrhiza-use, organic and mineral fertilizing on saturated hydraulic conductivity, porosity, aggregate stability and nitrate leaching were statistically significant (P<0.05). Organic fertilizing including compost, manure and mycorrhiza-inoculated compost significantly increased the aggregate stability while any effect of mineral fertilizing could not be found. The highest aggregate stability values at 0-30 cm soil depth were obtained with manure (37.84%), compost (33.86%) and mycorrhiza-inoculated compost (33.85%) applications, respectively. The increase in saturated hydraulic conductivity with compost application was 247% and 196% as compared to the control and mineral fertilizing, respectively. The manure increased saturated hydraulic conductivity compared with control and mineral fertilizing by 129% and 96%, respectively. Mycorrhiza-inoculated compost application also increased saturated hydraulic conductivity compared with control and mineral fertilizing by 116% and 84%, respectively. The effect of manure and compost applications at 0-30 cm on total porosity was similar to each other, and the increase in total porosity was 40 and 42% higher than that of mineral fertilizing and control, respectively. However, soil porosity was not significantly changed with mineral fertilizer application. Mycorrhiza-inoculated compost also increased total porosity by 27 and 29%, with regard to mineral fertilizing and control, respectively. The results revealed that compost, manure and compost+mycorrhiza applications significantly decreased NO3-N leaching as compared to mineral fertilizing; however, the highest NO3-N leaching among the organic applications occurred in manure application.