Australia is the largest per capita greenhouse gas emitter in the developed world. If it seeks to effectively contribute to its share of global climate change mitigation, it must make a transition from fossil fuels to renewable energy technologies and energy efficiency. Bioenergy is one renewable energy technology that could help to reduce Australia’s greenhouse gas emissions. Apart from being a low-carbon alternative to fossil fuels when it is produced in an environmentally sound way, it offers many other advantages. The Darling Downs, in south-east Queensland, is a large agricultural and energy-producing region, making it a suitable case study for examining the biophysical impacts of replacing fossil fuels with bioenergy alternatives. Stocks and flows modelling is ideally suited to this, as it allows for future alternative scenarios to be created that also examine the effects of the transition on various sectors of the economy. This thesis develops three scenarios to examine the impact of transitioning from fossil fuels to bioenergy on the Darling Downs. First, the base-case or reference scenario reflects current agricultural practices and energy generation. Second, the ethanol scenario involves the construction of four additional first-generation ethanol facilities. Even though it reduced the need for foreign fuel imports, thereby contributing to energy security, the feedstock requirements were beyond the production capacity of the Darling Downs making it untenable considering the importance of grain production within the region and concerns about sustainability/land use change. Third, the electricity scenario involves replacing coal partially or totally with biomass in the two existing coal-fired power stations in the region. Only this scenario saw a large decrease in greenhouse gas emissions; however, the large feedstock requirements resulted in a large decrease in grain production thereby requiring a level of cofiring between 10 and 100 per cent. It was also concluded that the expansion of bioenergy production on the Darling Downs would require modifications to the Large-scale Renewable Energy Target; the introduction of feed-in tariffs; increased support for bioenergy research and development; and the introduction of extension services for farmers to make it viable.