Invasive common reed (Phragmites australis) can rapidly form expansive, near-monotypic stands, and thereby lower plant diversity and change marsh habitat structure. Consequently, North American wetland managers often use herbicides, such as glyphosate-based AquaNeat® and imazypr-based Habitat®, to control its establishment and spread. However, herbiciding might indirectly affect benthic community structure by directly altering habitat structure, and habitat alterations may vary with herbicide and concentration. These effects may be particularly pronounced ≥1 year post-herbiciding when dead above-ground biomass collapses and submerges. To evaluate how herbicide-caused alterations in habitat affect key trophic linkages, we compared snail and epiphytic algal assemblages, and habitat conditions, among 20- × 20-m replicated plots of reed treated with either AquaNeat® (30 % solution), Habitat® (5 % solution), or left herbicide-free (i.e., controls) in an eutrophic Lake Erie coastal marsh 1-y post-herbiciding. Both herbicides equally reduced reed above-ground growth by >90 % relative to controls. Fossaria spp. and Gyraulus parvus snails were more abundant in herbicide-treated plots than in controls, but Shannon-Wiener diversity was similar (H′ ≈ 1.0) across treatments. All snails collected were pulmonates, suggesting habitat drying might be driving assemblage structure. Snails were denser in plots with metaphyton (mostly Spirogyra) than without, and metaphyton was more abundant in herbicide-treated plots with higher incident light levels and warmer water temperatures than in controls. Snail biomass was positively related to amount of benthic macro-organic matter but not epiphytic algal biomass, which was similar among treatments. Diatoms dominated algal communities in all treatments. In June, Navicula spp. was dominant in controls, whereas Nitzschia palea and Aulacoseira italic, and Nitzschia spp., were dominant in AquaNeat® and Habitat® treatments, respectively. However, algal and diatom assemblages were similar in treatments by early-July when marsh water levels significantly decreased and nitrate levels were <1 μg/L. Marsh hydrologic patterns may mediate herbiciding’s indirect effects on trophic structure.