Common carp, Cyprinus carpio, is a highly invasive fish species across freshwater systems of south-eastern Australia, and especially in semi-arid floodplain wetlands. However, multi-component, large-scale experimental studies on carp effects on such ecosystems are scarce. This is in spite of demands to prioritise management and control of carp for the rehabilitation of habitats across the Murray–Darling Basin. A 2-year, large-scale field experiment in a terminal wetland of the lower River Murray (South Australia) evaluated the effects of free-ranging carp on water transparency, aquatic macrophytes (biomass and cover), zooplankton density, benthic invertebrates (density, richness and diversity) as well as native fish. Within 1 year since artificial inundation, transparency sharply decreased and this was accompanied by a decrease in aquatic macrophyte biomass and cover, a fluctuation in zooplankton density, and a decrease in benthic invertebrate richness and diversity. Also, the decreases in transparency and benthic invertebrate richness were significantly related to carp biomass, which averaged 68.0 kg ha–1 and induced a shift from clear- to turbid-water state. Following a flood event, increased connectivity caused carp to further access the newly inundated areas.