In recent years, farming section of South Khorasan Province faces different limitations such as increasing shortage of water resources and continuous reduction of weather showers. Considering consecutive droughts and water crisis in agricultural plain of the province, it is necessary to use water resources optimally and increase productivity of water shortage input. Comparison of water productivity among the available utilization systems in agricultural section of the province can cause recognition of suitable and efficient utilization system for optimal use of water shortage input and increase water productivity in production of crops. In the present research, different indices of water productivity for production of crops in two small holding utilization system and Rural Production Cooperative in Khosef County have been calculated and compared. The required data have been collected with a sample of 247 farmers and with two-staged cluster sampling and with questionnaire. To calculate and compare water productivity, Benefit Per Drop, Crop Per Drop and Net Benefit Per Drop indices have been used. Results showed that the said indices were different for similar products in two utilization systems and in most crops, the said indices in rural production cooperative system were higher than small holding system. Therefore, gathering of smallholder’s farmers as rural production cooperative can lead to more desirable utilization of water resources and reduction of drought effects and water crisis.