The ecological status of subtropical floodplain lakes is threatened by eutrophication, which can shift lakes from a clear, macrophyte-dominated equilibrium state to a turbid, phytoplankton-dominated state. Such a shift is reflected in their macroinvertebrate assemblages, which may serve as good indicators of long-term changes in such lake ecosystems. We conducted a survey of benthic macroinvertebrates in 20 lakes in the Yangtze floodplain that were disconnected from the river channel to identify invertebrate response patterns along a gradient of eutrophication. Macroinvertebrate assemblages changed in parallel to the observed regime shift of a subgroup of those lakes. The most abundant groups were epiphytic invertebrates (e.g., Bithyniidae) in the macrophytedominated lakes and pollution-tolerant invertebrates (e.g., Tubificidae, Tanypus) in the phytoplankton-dominated lakes. Planktonic chlorophyll a concentration and wet biomass of submersed macrophytes were the key factors structuring macroinvertebrate assemblages. Macroinvertebrate taxon richness decreased along the eutrophication gradient, but density reached a minimum at a moderate eutrophication level and then increased. Scraper density (e.g., Bithyniidae) dropped abruptly at the moderate eutrophication level and did not increase again, whereas collector-gatherers (mainly Tubificidae and Chironomidae) and predators (e.g., Tanypus) increased continuously along the eutrophication gradient. We conclude that the abrupt disappearance of macrophytes during the regime shift means the loss of key habitat for biota associated with aquatic plants. Therefore, ecological restoration projects should be designed to reduce the nutrient concentration of floodplain lakes enough to allow re-establishment of a clear-water lake equilibrium dominated by aquatic macrophytes.