Serious droughts induced by expanding irrigation in the Aral Sea Basin have led to a reevaluation of water security in the region. At the same time, sustainable development in the region is coupled to water availability. Thus, creating a reliable estimate of future water demands is a top priority. Statistical modeling alone has not been consistently accurate with regard to modeling the impact of climate change on future water resources. We attempt to develop a physical water circulation model for the Aral Sea Basin, based on the land surface model SiBUC. To improve model performance, in situ measurements were carried out starting in 2011 at two sites in Kyzylkesek and Bayavut farms located in arid and semi-arid regions respectively. Soil moisture and electric conductivity, as well as ground water levels were measured in order to estimate actual irrigation application. Soil moisture in the arid farm sharply fluctuated due to high evapotranspiration and infiltration, while in the semi-arid farm it changed moderately. The semi-arid farm also showed an overall increasing trend of electric conductivity, corresponding to increased soil salinity over the period of observation. Finally, the local irrigation strategies were observed and reflected in the model, and irrigation frequency and annual water requirement for main cash crops were reproduced.