The Upper Mississippi River is thought to provide important stopover habitat for migrating landbirds because of its north-south orientation and floodplain forests. The river flows through the Driftless Area of southwestern Wisconsin and southeastern Minnesota where forests are plentiful, yet forests of the floodplain and Driftless Area uplands differ greatly in landscape setting, tree species composition, and topography. We compared landbird assemblages in these upland and floodplain forests over three springs, 2005–2007, using line-transect surveys at randomly selected areas in and within 16 km of the floodplain. We found more species of both transient and locally breeding migrants per survey in floodplain than in upland forest. Detections of transient neotropical migrants did not differ statistically by habitat. Detections of locally breeding neotropical and temperate-zone migrants and transient temperate-zone migrants were greater in floodplain than in upland forest. Between floodplain and upland forest, assemblages of locally breeding species, including neotropical and temperate-zone migrants (of which some individuals were in transit), differed substantially, but assemblages of transients (including both neotropical and temperate-zone migrants) did not differ as much. Only two species of transient migrants had clear affinities for floodplain forest, and none had an affinity for upland forest, whereas most locally breeding migrants had an affinity for either upland or floodplain forest. Within each spring, however, detections of transient neotropical migrants shifted from being greater in floodplain to greater in upland forests. This intraseasonal shift may be related to the phenology of certain tree species.