The Burdekin floodplain in Queensland, Australia, supports 80,000ha of sugar cane, with hundreds of km of irrigation drainage channels that move water around before reaching the ocean. The nutrient rich and turbid waters contribute to algal blooms, excessive aquatic weed growth and critically low dissolved oxygen black water events, which are often recorded in the floodplain waterways. Various fish and habitat surveys have been undertaken between 2004 to 2018, presenting an opportunity to collate these data to examine whether fine scale patterns exist in the fish assemblages across the floodplain, and to also test the drivers of these patterns. A total of 42 species, representing 26 families, are reported. Sixteen species are diadromous, having a lifecycle ecology requiring floodplain connection for movement to estuaries. Our results reveal that each floodplain creek has a different fish assemblage, which means that fine scale barriers to movement and connectivity, and habitat conditions, are disrupting fish productivity. We advocate that the transferability of understanding and restoration approaches from one system to another, even for the same floodplain, is more difficult than assumed. This presents a central challenge for managers when implementing restoration programs that have broader nature positive targets.