Worldwide estuaries have been subject to multiple and escalating anthropogenic impacts which have resulted in the loss of many ecosystem goods and services including: commercial activities, navigation and marine transportation, recreational and landscape values, and flood control and biodiversity support. An example of these losses is provided in an urban-industrial region of an estuary in northern Tasmania, Australia, where excessive silt deposition has resulted in almost complete loss of the channel at low tide. The causes of siltation have long been attributed to poor watershed management and high concentrations of flocculated and suspended sediments transported upstream by asymmetrical tides. However, historical analysis of anthropogenic changes in estuarine and riverine processes revealed different stressors. These included the decrease in the tidal prism and hence regime equilibrium, brought about by channel infilling and draining of tidal wetlands to create dry land for urban and agricultural uses, and the reduction and redirection of freshwater inflows for the generation of hydroelectricity. Watershed sediment loads exerted a relatively minor role in the estuarine equilibrium, which is solely dependent on tidal flows and river discharges for maintenance of stable cross-sectional areas. Sustainable remediation measures include increasing the tidal prism through the restoration of dynamic river flows and reconnection and restoration of tidal wetlands. However, the former will not be achievable without changes in major provisioning services, particularly the use of water to generate hydroelectricity. This study emphasises the importance of identifying stressors as the basis for examining the potential to reduce the trade-offs between the multiple ecosystem services provided by an estuary and its tributaries, particularly between provisioning and cultural ecosystem services, within a rehabilitation context.