It is a fact that a focus on sustainability must be taken into account in all processes, including those addressed in this book. This chapter gives a broad overview of the current environmental crisis humanity is facing, putting special emphasis on the impact of biofuel production according to a classification based on generations. Considering this, the potential benefits of microalgae biofuels are discussed. A definition for sustainable development is given. Industrial ecology and ecological economics are described as two approaches for sustainability implementation in the context of any production system. Several tools for sustainability measurement are also described in the context of biofuel production; these are: life cycle assessment, ecological footprint, carbon footprint, indicators sets and cost benefit analysis. As an example of the application of such tools, a case study on biodiesel production from microalgae is presented