The production of alternative transportation fuels is imperative to meet future energy demands without contributing to global climate change. Advances in alternative processing techniques that have emerged due to interest in microalgae as a feedstock have led to a variety of potential processing pathways for the production of bio-based fuels. A major hurdle in the algal production process is maintaining a fast and stable algae culture. Monocultures, developed for their high lipid content, suffer from low productivity, are susceptible to crashes and require a constant supply of carbon dioxide to maintain productivity. In an effort to circumvent these obstacles, algal turf scrubber systems (ATS) are now being targeted not only for water purification, but as a means of producing algae feedstocks for fuel conversion. The resulting algae are capable of being harvested at a much higher density, requiring less energy for dewatering purposes. ATS systems do present other drawbacks that downstream technologies need to account for to make this system a viable means for fuel conversion. While polyculture algae species display great growth characteristics, they contain high percentages of nitrogen containing proteins and low lipid content. If not removed this nitrogen pollutes any resulting biocrude making it unacceptable for diesel fuel blends. This study investigates a processing method which reduces the nitrogen content of the resulting fuel by fermenting both carbohydrates and proteins into intermediate compounds. By tuning the E. coli fermentation stain it is hoped that the process will yield higher value co-products than those investigated in this study. The research contained herein incorporates laboratory experimentation with engineering systems modeling to assess the economic feasibility and environmental impacts of generating biofuels from ATS cultivated algae. Results show a minimum fuel selling price of $5.93 per gasoline gallon equivalent and greenhouse gas emissions of -0.0185 kg CO2eq per MJ fuel. Discussion points include process optimization in terms of minimum fuel selling price and global warming potential.