Like other major river basin systems in the West of the United States the Platte River Basin are faced with the challenges of allocating more water for plant and animal species. A part of the Central Platte River was designated as critical habitat for the whooping crane in 1978. The water allocation system in the Platte River Basin is dominated by the Prior Appropriation Doctrine, which allocates water according to the priorities based on the date of water use. The Platte River Basin segregated into five subregions for purpose of analysis. 24 years of historic records of monthly flow and all the demands were complied. The simulation of river basin modeling includes physical operation of the system including water allocation by water rights and interstate compact agreements, reservoir operations, and diversion with consumptive use and return flow. MODSIM, a generalized river basin network model, was used for estimating the timing and magnitude of impacts on river flows and diversions associated with water transfers from each region. A total of 20 alternatives were considered, covering transfers from each of the five regions of basin with several options. The result shows that the timing and availability of augmented water at the critical habitat is not only a function of use by junior appropriators, but also of river losses, and timing of return flows.