Cotton is the main crop in Uzbekistan. The use of water for irrigation of cotton has a number of environmental consequences, most notably the decreasing of the Aral Sea, and triggering water salinity increase. Modeling of water management for cotton production in the cotton agro-eco zones of Uzbekistan is a challenge constrained by the availability and salinity of water. This research presents a system dynamics model of water management for cotton production in Uzbekistan. Causal loop diagram and stock flow diagram are hypothesized to generate the observed behavior of cotton production system. The model was programmed using the software STELLA and was solved using Runge–Kutta forth order method. Simulated results agree well with the observed data of cotton area and total cotton production quantitatively. Sensitivity analysis of the model have also been addressed. Also the model has been simulated to address the policy issue of investment on drip irrigation, cotton price liberalization, improvement in crop productivity and a mix policy which is combination of these three policies. Finally, the model provides better understanding and greater insights for water management of cotton production for better management of cotton production and can be used as a computer laboratory for scenario building and policy analysis.