Invasive species have many detrimental ecological and socio-economic effects. However, invasive species can also provide novel habitat for native species. The growing rate of biological invasions world-wide presents an urgent dilemma: how can natural resource managers minimize negative effects of invasive species without depleting native taxa that have come to rely on them? Adaptive management can provide a means to address this dilemma when invasive species management plans are crafted in novel environments. We present a case study of research in support of adaptive management that considers the role of invasive water hyacinth (Eichhornia crassipes [Mart.] Solms [Pontederiaceae]) management, using herbicides, in aquatic food web functioning in the Sacramento–San Joaquin River Delta of California, USA (the “Delta”). We hypothesized that herbicide applications under current management protocols would reduce the abundance and diversity of aquatic invertebrates because they would alter both structural and biological habitat. Using a Before, After, Control, Intervention (BACI) experiment, we sampled invertebrates per gram plant biomass before and 4 weeks after glyphosate applications in treated and untreated locations. There was more plant biomass in the late-season samples because dead, dying, and living plant materials were compacted. However, there were no detectable differences between control and treated sites — or for samples before versus after the treatment date—for invertebrate abundance, species richness, or evenness. This case study demonstrates that even decaying water hyacinth serves as habitat for invertebrates that may be forage for Delta fishes. We concluded that current management practices using glyphosate do not affect invertebrate abundance during a month-long period of weed decay. These results provide valuable feedback for the “evaluate and respond” component of the adaptive management process for water hyacinth control, and demonstrate how managers globally can and should consider potential food web effects in the course of their invasive species management efforts.