New environmental policies motivate the efficient production of biofuels. Despite their potential, biofuels based on microbial biomass cultivation are not cost effective yet due to the low biomass productivity of raceway ponds. To improve the performance of raceway ponds, better process models are needed. In this paper, a raceway pond model incorporating genome-scale metabolic reconstructions is presented. This process model is used to simulate different production scenarios such as an algae monoculture with flue gas sparging and algal/yeast/bacterial consortia growing on glucose and xylose. The simulations predict that the consortia process alternatives could achieve a production cost in the range of $3.81/litre to $16.16/litre of biodiesel. This is important because while algal growth on flue gas is only economic in the proximity of carbon dioxide sources, microbial consortia growing on lignocellulosic waste can be implemented in many more locations.