Abstract Coastal wetlands provide critical habitat for aquatic organisms and important ecosystem services for the terrestrial and aquatic landscapes that they bridge, but increasingly common invasive macrophytes disrupt plant communities, food webs, habitat structure and littoral–pelagic linkages. In Laurentian Great Lakes coastal wetlands, invasive cattails (Typha × glauca and T. angustifolia, hereafter Typha) homogenise ecosystem structure and reduce nearshore dissolved oxygen, and plant, fish and macroinvertebrate diversity. We hypothesised that management treatments which reduce Typha and its abundant litter promote structural heterogeneity and mitigate physicochemical and biodiversity impacts. To test this hypothesis, we implemented a large‐scale (2,048 m2 treatment units), multi‐site (four coastal wetlands) experiment in northern Michigan (U.S.A.) to examine how invasive Typha mechanical harvesting treatments (biomass harvest, aquatic connectivity channels, Typha‐dominated control) altered fish, macroinvertebrate, plant, larval amphibian abundance and diversity, and water quality for 2‐year post‐treatment. Both harvest and channel treatments reduced Typha biomass, cover and dominance; harvest increased multi‐taxa species richness, fish diversity and abundance; and channels altered plant, fish, and macroinvertebrate community structures. Dissolved oxygen was greater and litter was reduced by both treatments, indicating likely mechanisms for shifts in fish and macroinvertebrate use. Our results suggest that harvesting invasive macrophytes can ameliorate biodiversity impacts and improve habitat quality, and that adding aquatic connectivity channels can increase community complexity. Typha management that incorporates both harvesting and aquatic connectivity channels appears to provide the greatest benefit to several taxonomic groups, likely by reducing Typha and its litter, increasing dissolved oxygen availability, and increasing the connection between open water and wetland interiors. Increasing habitat complexity and aquatic connectivity of invaded wetlands can promote biodiversity and provides a more realistic management goal than the complete elimination of invasive macrophytes.