The potential impacts of irrigation development on tropical Australian floodplains and fish communities is an issue of current interest considering proposals to further develop water resources in northern Australia. Studies examining risks associated with further water resource development have focused primarily on Australia’s undeveloped northern river basins but could benefit from examining long established irrigation areas on seasonally dry tropical floodplains in north Queensland. The lower Burdekin river floodplain is intensively developed to irrigated agriculture producing about a quarter of Australia’s sugar cane crop. It has a high level of hydrological modification including the use of historically seasonal floodplain distributary channels as conduits for the supply or irrigation water and shallow aquifer recharge operations. The loss of hydrological seasonality and other catchment and basin scale impacts has led to extensive submerged macrophyte and aquatic weed infestation and associated water quality decline. Conditions become most chronic during wet season flow events preventing recruitment of catadromous fish species from estuarine to floodplain habitats. In this presentation we examine the integrated causes of water quality fish passage barriers, broader ecosystem risks associated with high BOD in floodplain distributary wet season flows and potential adaptive management options.