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The overall goals of this research are to identify forms of environmentally friendly microalgal biodiesel production and to address the broader policy implications of the Renewable Fuel Standard 2 (RFS2) to avoid unintended environmental consequences from the production and the utilization of biofuels. Life cycle assessment (LCA) of microalgal biodiesel was conducted using a process LCA model with Monte Carlo Analysis (MCA) for uncertainty analysis. First, the study focused on environmental impacts from the production of microalgal mass. Twenty scenarios of microalgal cultivation with different sources of CO2, nutrients and material used to construct photobioreactor (PBR) were evaluated. The results showed that the utilization of CO2 from flue gas only reduces global warming potential (GWP), while the utilization of nutrients from municipal wastewater mainly reduces eutrophication potential (EP), and the selection of material used to construct PBR is important. LCA of microalgal biodiesel was conducted to evaluate the major contributions to different environmental impacts and to identify the production condition with minimal impacts. Environmental impacts from four different microalgal biodiesel production scenarios to achieve the biomass-based diesel quantity required by the RFS2 were quantified. These four scenarios included lower and higher production efficiencies and different sources of resources, which are synthetic, and natural and waste. None of the four scenarios met the RFS’s greenhouse gas emissions requirement. The emissions can be minimized by improving the energy efficiency of harvesting process, since the GWP results are sensitive to energy consumption in harvesting process. Sensitivity of EP, ozone depletion potential and ecotoxicity potential to other parameters are also reported. GWP, EP and photochemical smog formation potential (PSP) results from the scenario with minimal impacts were compared to the impacts from other diesels, petroleum diesel, soybean diesel and canola diesel. The tradeoffs between different types of diesel suggested that future RFS should include other environmental criteria such as EP and PSP to minimize unintended consequences. Possible strategies to setting life-cycle EP and PSP criteria are discussed. Finally, a LCA on the co-production of microalgal biodiesel and bioethanol from microalgae and corn were conducted. CO2 for microalgal cultivation was provided from flue gas and/or fermentation processes. The recovery of CO2 from fermentation process decreases GWP, but slightly increases EP. The co-production of the microalgal biofuels can reduce GWP and EP by 54 and 52%, respectively, compared to the production of microalgal biodiesel alone. Lipid and carbohydrate contents of microalgae should be 24-36% and 44%, respectively, in order to produce the maximum energy content in algal biofuels with the minimum GWP and EP impacts.