The conclusions from life cycle assessment of algal biofuels (e.g., biodiesel, renewable diesel) vary significantly due to both modeling and inherent technological uncertainties. The inherent uncertainties of US-based algal biofuels production were investigated by eliminating modeling uncertainty via comprehensive harmonization through a meta-analysis. Following harmonization, the cumulative fossil energy consumption (MJ/MJ), global warming potential (g CO2-eq/MJ) and water consumption (m(3)/MJ) of different algal biofuel process trains were investigated through a stochastic life cycle model. By focusing on the inherent differences of current technologies, this study identified (1) the differences in impact results between different process trains (i.e., different combinations of technology choices along the fuel production life cycle), (2) high impact hotspots, and (3) possible low impact process trains, all of which are crucial to further improve the sustainability of algal biofuels. The median (range) values of the three indicators for the most common algal biodiesel process train are 3.5 (2.9-4.2) MJ/MJ, 99 (55-151) g CO2-eq/MJ and 0.08 (0.07-0.09) m(3)/MJ, with corresponding inter-quartile ranges being 63%, 46% and 43% less than the literature values, respectively. The median (range) values of the three indicators for the most common algae renewable diesel process train are 1.7 (1.4-2.2) MJ/MJ, 84 (60-112) g CO2-eq/MJ and 0.04 (0.03-0.05) m(3)/MJ, with the corresponding reductions in inter-quartile range by 83%, 83% and 84%, respectively. Although neither of the median global warming potential results for algal biofuels met the mandatory thresholds in the Renewable Fuel Standard (45 g CO2-eq/MJ), it is possible to meet the requirement by integrating low impact technology options into the process trains.