There is significant evidence demonstrating that altering river flows downstream of impoundments harms native aquatic ecosystems and decreases the ability of native species to strive and survive. Innovative water management practices are needed to improve the health of native aquatic species and their surrounding ecosystems while maintaining the benefits from historic operating policies at these facilities. The impacts of individual reservoir operations on ecosystem health are often masked by the compounding influence of multiple upstream impoundments, making it difficult to analyze an individual facility’s impact within the larger system. This study presents an optimization model that investigates the value of coordinated reservoir management practices for ecological benefits in a dynamic system with several major reservoirs operating for hydropower production. An application of this model is presented for five hydropower facilities along the Connecticut River using The Connecticut River Environmental Assessment Model (CREAM). The Connecticut River Basin is the largest river basin in New England and one of the most impounded rivers in the United States. Five hydropower facilities along the Connecticut River are undergoing Federal Energy Regulatory Commission (FERC) re-licensing.