The impact of the eutrophication of the Great Barrier Reef has received increasing attention in the literature and media. There is great interest in the effects of eutrophication on the macroalgae-coral community, and its impact on the reef and associated industries such as fisheries. Therefore, this thesis presents a model which evaluates the impact of agriculture on fisheries, and examines different policy options available to the government. The model presents a dynamic game of the linkage between agriculture and fisheries based on the "lake game" literature, linking cane production in the Burdekin Region with the fisheries industry operating in the Great Barrier Reef through a damage function. As the amount of nutrients and sediments is dependent on the water flow, which can vary depending on rainfall patterns, a model of river flow is essential for studying the impact of agriculture on the Great Barrier Reef ecosystem. It is well established that stream flow is persistent, and an indication of the level of persistence can be gained from Hurst's work. Therefore, the Hurst exponent is calculated and used to develop a river flow simulation model based on fractional Brownian motion; these simulated values for annual runoff have then been integrated into the bio-economic model. Under the assumption of a dynamic Stackelberg equilibrium the model is solved. Firstly, the farmers' utility is maximized subject to the dynamics of nutrient runoff using optimal control theory, and then the profit function of the fishermen is maximized subject to the dynamics of the fish stock, again using optimal control theory. The coupled nature of these optimal control problems results in the model being a dynamic game. Finally, the model is used to analyse the effects of different policy options by altering the parameter values.