A Decision Support System (DSS) was developed for the reservoirs operated by the U.S. Bureau of Reclamation that incorporates biological resources in a palette of decision variables. A scoring technique was developed for the DSS to help to evaluate the long-term effects of proposed reservoir system operations on those variables. The biological component of the DSS was developed to help Bureau of Reclamation reservoir operators evaluate the effects of different scenarios of reservoir operations on a variety of water-related biological resources. In this DSS, Reclamation's Reservoir Operations Modeling System (ROMS) is linked to modules evaluating power production, flood control benefits, irrigation water deliveries, municipal and industrial water supplies, habitat for endemic fish communities, tailwater fisheries, nesting habitat for shorebirds, reservoir recreation, reservoir fisheries, and regeneration of riparian cottonwood forests. Operation scenarios generated in ROMS are scored for each decision variable by comparison to a target range of a decision variable for a reference location and time period. The score for a variable is calculated based on the ratio between the percent of time that target conditions are met under alternative operating conditions and under the reference condition, respectively. A scoring technique was developed that recognizes that under either natural or highly managed conditions the reference target is not met at all times. Higher scores are achieved for environmental decision variables by operations scenarios that approach natural seasonal and annual variability in habitat availability.