Hydrological changes associated with irrigation, in conjunction with increased nutrient concentrations and aquatic plant densities, have greatly impacted fish habitat values on the Burdekin River floodplain. The two most significant weeds in the Burdekin floodplain are water hyacinth (Eichhornia crassipes) and para grass (Urochloa mutica). Water hyacinth creates a base for the para grass (and then other weeds) to grow out into deeper water, creating weed mats that can then only be removed by mechanical means or floods of the largest magnitude. We attempted to rehabilitate floodplain lagoons by the mechanical removal of floating weed mats and monitored the result by measuring the subsequent effects on fish habitats and fish communities. Prior to weed removal, fish habitats were generally of poor quality, and fish community structure was skewed away from rich native assemblages to depauperate communities dominated in some instances by alien species. Poor water quality arising from floating weed mats is considered to be the main determinant of reduced fish abundance and diversity. After mechanical weed removal, recovery of water quality and physical habitat led to the re-establishment of many native fish species. Key refuge habitats within the distribution channels were a critical source of recruits for fishes dispersing during times of elevated seasonal flows into the newly rehabilitated reaches. This study demonstrates that floating alien weed mats have significant negative effects upon aquatic communities and that mechanical removal of these weed mats (as opposed to chemical removal) results in dramatic improvements in native fish species richness and abundance.