The upper Mississippi River is managed as a multiple use system, balancing the needs of industry, recreation, and navigation. Through water-level management (WLM), the U. S. Army Corps of Engineers manipulates water levels in some navigation pools to promote emergent vegetation for fish and wildlife in off-channel habitats. A manipulative experiment was conducted to assess responses of invertebrates to vegetation and associated organic matter associated with WLM in floodplain wetlands of Mississippi River navigation pool 25. Macroinvertebrate and zooplankton communities and benthic organic matter were compared in replicated paired plots consisting of experimentally de-vegetated and adjacent control plots. Hydrology was variable during the study, resulting in a strong vegetation response year (1999), a no response year (2000), and a moderate response year (2001). Differences in benthic organic matter between plot types were most pronounced in fall 2000, following the strong vegetation response year, where residual vegetation resulted in significantly higher total and coarse benthic organic matter in vegetated plots. Of the 2 years (2000, 2001) they were sampled, differences in macroinvertebrate communities were only evident in 2001 when there was a moderate vegetation response. Total macroinvertebrate densities during 2001 were similar between devegetated and vegetated plots, but responses of individual taxa varied. Total macroinvertebrate biomass was significantly higher in the vegetated plots during 2001. Of dominant groups, Oligochaeta biomass was significantly higher in vegetated plots, whereas total Chironomidae abundance and biomass were both significantly higher in devegetated plots. Community metrics reflected higher macroinvertebrate diversity in vegetated plots. Zooplankton were not abundant or diverse in plots, but total densities were significantly higher in vegetated plots during the 1999 strongest vegetation response year. Results demonstrate that WLM to enhance emergent vegetation in off-channel habitats of this large river influences organic matter dynamics and invertebrates. Although many groups responded positively to vegetation, responses varied with the degree of vegetation response and the taxonomic resolution of analyses, suggesting that hydrologic variability, and associated spatial and temporal variability in emergent vegetation, can enhance invertebrate diversity in floodplain wetland habitats.