This paper addresses uncertainty in socio-economic and sediment-nutrient models that are being developed for the assessment of change in the Great Barrier Reef (GBR) area. The catchments draining into the GBR lagoon are sources of pollutants. The Reef Water Quality Management Plan of the Queensland Government identified sediments and nutrients transported to the GBR lagoon as the major long-term threats to the reef and inshore ecosystems and the wellbeing of the human communities. The plan clearly indicates that changes in land management are required by 2013 to reduce pollutant inputs and, at the same time, maintain or enhance the benefits from using the inland waters. Science that provides decision tools for natural resource management and improves socio-economic and biophysical understanding is required to enable managers to make better decisions. A major research activity (the Water for a Healthy Country Flagship) aims to address social, economic and biophysical outcomes of land management change in the GBR. It contains research activities that provide information for integrated model development. Currently, however, these models lack the ability to estimate the uncertainty associated with prediction. This project aims to provide statistical methods for assessing uncertainty in models of sediment transportation to the GBR. Furthermore, it provides a link between the models and the decision-making process that allows assessment of uncertainty, a step pertinent to the risk analysis of policy options. This paper describes current and ongoing approaches for assessing uncertainty using a sediment modelling example and provides a way forward for the integration of applied socio-economic and biophysical models used in the decision-making process.

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