Human disturbance can negatively impact the linkage of riparian and aquatic food webs in numerous ways, including by separating riparian vegetation from the stream channel. One consequence of this separation may be reduced allocthonous input of organic material from the riparian area into the stream. We tested whether surface water withdrawals associated with irrigation diversions impacted the connection between riparian vegetation and the stream channel in a fifth order river, and measured the result of this separation on allocthonous inputs of riparian invertebrates into the river. The study was conducted on a 29 km stretch of the Umatilla River in eastern Oregon, where four in-stream structures divert surface flow for irrigating croplands. Water withdrawal is maximized in late summer, and in 2006, the structures reduced in-stream flow by more than 97%. The position of the active stream channel relative to riparian vegetation was measured under high flow conditions in June and, again, in August. Allocthonous input into streams was measured in August using pan traps at four pairs of sites, with one site of each pair located above a diversion structure, and one site below. Pan traps were left open for one week. Invertebrate input, as measured by the number of individuals, was significantly higher above diversions than below. This result may be due to the separation of the stream channel from riparian vegetation; the distance that the river channel moved away from riparian vegetation at each site from July to August was significantly negatively correlated with the number of invertebrates in pan traps at each site.