Shallow water habitat (SWH) is important for riverine fish and their invertebrate prey, yet the availability of SWH has declined in many systems due to human impacts. We evaluated the potential ecological benefits of restoring SWH by comparing zooplankton and phytoplankton from created backwaters (a floodplain feature connected to the river on the downstream end but disconnected at the upstream end) and chutes (a side channel of the river that diverts flow from the main channel through the chute and back into the main channel) on the lower Missouri River. We tested the hypothesis that backwaters support higher abundances of zooplankton and phytoplankton than chutes using data that were collected during the summer of 2010. As predicted, backwaters had more diverse cladoceran communities and greater abundances of rotifers, copepod nauplii, adult copepods, and cladocerans than chutes. Total algal biovolume was the same in chutes and backwaters; however, phytoplankton taxa richness was higher in backwaters, and there was a greater biovolume of green algae (Chlorophyta), Crypotophyta, cyanobacteria, and Euglenophyta in backwaters than in chutes. Differences in zooplankton and phytoplankton between backwaters and chutes appeared to be related to slower current velocities, longer retention times, and lower levels of turbidity and total suspended solids in backwaters. While chutes have the potential to provide greater habitat diversity than the mainstem, there were no differences in water quality or phytoplankton abundance, community structure, or diversity between these two habitats. Combined, our results suggest that created backwaters initially provide a greater potential food resource for native fishes. However, additional research is needed to determine whether chutes can also develop beneficial shallow water features over a longer period of time.