The flow regime of the Connecticut River Basin (CRB) has been markedly altered due to the high number of impoundments reservoirs in the basin. The major services provided by these reservoirs include hydropower production, water supply, recreation and flood control. The United States Army Corps of Engineers (USACE) operates 14 flood control facilities within the basin. The storage capacities of these facilities range from 3,740 to 71,000 acre-feet. USACE is currently exploring operational alternatives that include both traditional economic benefits of the reservoirs and benefits of returning the flows of the Connecticut River and its tributaries to a more natural flow regime. A daily time-step optimization model was created to evaluate the tradeoffs between the Connecticut River’s natural environmental services and its reservoirs’ multiple uses. This paper evaluates the relationships between flood control and environmental flows for aquatic species and floodplain health. Environmental flow targets, developed by aquatic scientists, biologists, and other stakeholders are used to evaluate deviations from natural flows for each ecological species of interest, for each month of the year, at critical locations throughout the basin. This paper investigates case studies on two tributaries to the Connecticut River: the West and Ashuelot. The results of this study indicate that flows in these two rivers can be returned to a more natural flow regime without significantly increasing the occurrence of flooding by adjusting existing operational storage and release targets.