The invasive strain of the common reed, Phragmites australis, has negative impacts on wetland habitats and, thus, has been subject to various control strategies. Given the importance of plant detritus in wetland ecosystems, we investigated how treatment of P. australis with the herbicide, glyphosate, affected detritus quality and decomposition rates, bacterial and fungal biomass, and macroinvertebrate colonization. Responses were measured during a litter decomposition experiment using herbicided and non-herbicided Phragmites australis and, for comparative purposes, a native wetland sedge, Scirpus cyperinus (woolgrass). In spite of differences in fungal and bacterial biomass between herbicided and non-herbicided Phragmites, there were no differences in decomposition rates or leaf chemistry (C:N ratio) among these treatments. Furthermore, in spite of differences in the microbial community, abundance of macroinvertebrate functional groups (e. g., numbers of collector gatherers) and dominant taxa (chironomid midge larvae, ostracods, oligochaete worms, talitrid amphipods and planorbid snails) did not differ between treatments. Therefore, use of glyphosate herbicide on Phragmites appears to not have a strong litter-mediated impact on invertebrate food web structure. In addition, Phragmites litter decomposed faster and had higher invertebrate richness than native Scirpus. Macroinvertebrate numbers and taxa richness were positively correlated with bacteria numbers and were higher on both types of Phragmites litter than Scirpus litter. Thus, potential changes in wildlife and fish communities caused by herbicide control of invasive Phragmites are more likely to be mediated via modifications of species composition or physical structure of the wetland plant community than direct impacts of the herbicide on detrital trophic pathways.