Abstract: Whenever good quality water is scarce, water of marginal quality will have to be considered for using in agriculture. Municipal waste water is marginal quality water and using of this for irrigation can be an important consideration when its disposal is being planned in arid and semi-arid regions. In this study, secondary municipal effluent was used for irrigation of tomato. This effluent is using activated sludge process to treat the municipal wastewater. Five different irrigation treatments were designed with three replications. The treatments were as follows: T1: Furrow irrigation with drinking water network. T2: Surface drip irrigation (DI) with treated wastewater. T3: Sub surface drip irrigation (SDI) in 15 cm depth with treated wastewater. T4: Sub surface drip irrigation (SDI) in 30 cm depth with treated wastewater. T5: Furrow irrigation with treated wastewater. Crop water requirement was determined by ET-HS model. Also, in this study, chemical and microbiological characteristics of soil, water and crops have been analyzed. The results of this study indicated that application of DI and SDI could be control environmental contamination and in comparison surface irrigation, decreases the pollution problems in the soil. Also, the highest yield was obtained from T2 and T3, which was about 52 tons ha-1 (18 tons ha-1 higher than the average yield of the T1). A part of this increased yield can be related to better soil moisture and increased available nitrogen in the root zone. Additionally, with regard to health problem, minimum contact was generated between the effluent and the workers or the aerial plant parts. But the microbiological tests indicated that among of effluent treatments, T3 had better microbiological quality of tomato.