A representative agricultural area of 150 ha located in a protected ecosystem (Axios River Delta, Thermaikos Gulf-N. Aegean, Greece) was selected in order to investigate water quality parameters [pH, electrical conductivity (EC(w)), NO(3)-N, NH(4)-N, total phosphorus (TP)] in irrigation and drainage water. In the study area, the cultivated crops are mainly rice, maize, cotton, and fodder. Surface irrigation methods are applied using open channels network, and irrigation water is supplied by Axios River, which is facing pollution problems. The return flow from surface runoff and the surplus of irrigation water are collected to drainage network and disposed to Thermaikos Gulf. A 2-year study (2006-2007) was conducted in order to evaluate the effects of land use and irrigation water management on the drainage water quality. The average pH and NO(3)-N concentration was higher in the irrigation water (8.0 and 1.3 mg/L, respectively) than that in the drainage water (7.6 and 1.0 mg/L, respectively). The average EC(W), NH(4)-N, and TP concentration was higher in the drainage water (1,754 muS/cm, 90.3 microg/L, and 0.2 mg/L, respectively) than that in the irrigation water (477.1 muS/cm, 46.7 microg/L, and 0.1 mg/L, respectively). Average irrigation efficiency was estimated at 47% and 51% in 2006 and 2007 growing seasons (April-October), respectively. The loads of NO(3)-N in both seasons were higher in the irrigation water (35.1 kg/ha in 2006 and 24.9 kg/ha in 2007) than those in the drainage water (8.1 kg/ha in 2006 and 7.6 kg/ha in 2007). The load of TP was higher in the irrigation water in season 2006 (2.8 kg/ha) than that in the drainage water (1.1 kg/ha). Total phosphorus load in 2007 was equal in irrigation and drainage water (1.2 kg/ha). Wetland conditions, due to rice irrigation regime, drainage network characteristics, and the crop distribution in the study area, affect the drainage water ending in the protected ecosystem of Thermaikos Gulf.