Australia has embarked on a significant, and expensive, environmental flows program to restore the ecology of the Murray-Darling Basin. Such high stakes decisions will be audited on the basis of the benefit returned from the cost of the outlay and the opportunity costs of reduced water allocations to industries and communities dependent on irrigated agriculture. These restoration programs have been underpinned by the focus on river flows as the cause of system degradation. A longer term view of ecosystem condition identifies the flux of sediments, salts and nutrients as significant drivers of wetland change, albeit exacerbated by the regulation of river flow and the changed hydrological setting of associated floodplain wetlands. These long term records also attest to the rapid infilling of shallow wetlands and their likely terrestrialisation in the absence of future scouring flows. They also reveal regime shift changes driven by changes to the light environment from chronic high water turbidity. Further, sediment source studies reveal river water to be a principal vector for the continued supply of fine sediments to wetlands questioning the anticipated wetland recovery from watering. Investment in the mitigation of sediment flux is essential if the community is to reap the full benefits of the allocation of contested water volumes to the environment.