This paper describes a modelling tool that integrates Material Flow Analysis, energy production and Greenhouse Gas (GHG) emissions accounting for biomass flows at a regional scale. This tool allows comprehensive analysis of alternative systems for management of biomass waste and bioenergy production in regional areas. Different possible options for processing a range of biomass waste streams can be evaluated against multiple criteria including various environmental impacts and cost-effectiveness. The objective is to support the design of integrated biomass waste and bioenergy systems that maximise synergies and optimise tradeoffs between bioenergy production, GHG emissions, recycling of valuable soil nutrients and control of harmful contaminants. This analytical tool is applied to a major agricultural region in Australia, the Murrumbidgee Irrigation Area. A scenario demonstrates how the construction of different types of bioenergy plant can offer valuable benefits with regard to renewable energy production, GHG emission reductions, increasing phosphorus cycling back to soils and reduced cadmium contamination.