Last decade has seen reduction of amount of fossil raw materials for production of conventional fuels that in turn has been accompanied by deepening of the environmental problems. There is a trend of biofuel production rise accompanied by increase of the amount of waste produced. The waste is classified as productive (i.e. technological) one and operational one (for utilization of biofuels and their value). The study is focused on the creation of tools for supply chains (SC) by description/formulation of optimal management of production and operational waste. Tools are developed for production and use of biofuels that include a mathematical model and its optimization. The procedures are based on the following criteria/conditions: known production technology, spatial distribution logistics and production units and environmental pollution by waste fuel gases containing prevailingly CO2. The SC building also aims to provide the necessary fuel quantities for heating and transport systems as well as to foresee their optimization in terms of the environmentally-friendly aspect.