Restoration of the Atlantic salmon (Salmo salar) to New England rivers requires, in part, an understanding of the use of habitat and prey by potential and known predators. We examined variation in habitat use by Double-crested Cormorants (Phalacrocorax auritius), from April through June 1992-94 on ca. 288 km of the 2 primary tributaries and the mainstem of the Penobscot River, Maine. Our objectives were to quantify temporal and spatial variation in habitat use and test for selection of spring foraging habitats by cormorants. Cormorants forage during daylight hours only. To determine the distribution of foraging birds we conducted aerial surveys at intervals of <8 days. Counts from individual aerial surveys were analyzed relative to 9 river sections and used to examine selection of foraging habitats, such as free-flowing areas and the headponds and tailraces of dams. We defined selection as the difference between the proportionate length of each river section relative to the total river km available and the observed proportion of birds using each section. All birds observed from the aircraft within a river section were assumed to be foraging within that river section. Cormorants were first observed between 15 and 20 April in all 3 years. Individuals consistently selected (P < 0.05) against use of 2 large tributaries and sections >105 km north of the mouth of the mainstem. However, from late April through early June of all years, birds selected (P < 0.05) 4 of the 5 mainstem dams and the estuarine portion of the river. Cormorant use of dams remained at or above expected levels until the second week of June in all years. We suggest that cormorant selection for foraging areas adjacent to dams reflected a higher availability of prey, possibly due to delay and injury of migrating Atlantic salmon smolts. Cormorant selection of the estuarine portion of the Penobscot River was likely a response to a seasonally increasing availability and abundance of estuarine and marine prey, in addition to resident freshwater species and migrating smolts.