The estuarine mysid, Neomysis mercedis, has colonized John Day and other run-of-the-river Reservoirs of the Columbia River, over 400 km from the estuary. In John Day Reservoir N. mercedis numbers peaked (2 m-3) in August in areas near the dam in association with lower water velocity and softer bottom than at the upstream sampling sites. Neomysis broods were primarily released in late spring and early fall. Gut content analysis showed that Neomysis feeds mostly on cladoceran zooplankton and rotifers in John Day Reservoir. Diel vertical migration was documented, with daytime distribution restricted to the bottom and preferentially to the soft-textured sediments in the deepest areas. Common pelagic fishes in the reservoir, especially juvenile American shad (Alosa sapidissima) and chinook salmon (Oncorhynchus tshawytscha), are daytime zooplankton feeders that cannot prey on Neomysis owing to mysid diel vertical migration. Thus, Neomysis has become an important food web component in John Day Reservoir. We also collected N. mercedis further upstream in Lower Granite Reservoir, where another estuarine crustacean, Corophium salmonis, also is reported, underscoring the need to better understand the role of these estuarine invertebrates in the trophic ecology of the Columbia River. Copyright ?? 2006 John Wiley & Sons, Ltd.