Integration of wastewater treatment with algae cultivation is one of the promising ways to achieve an economically viable and environmentally sustainable algal biofuel production on a commercial scale. This study focused on pilot-scale algal biomass production system development, cultivation process optimization, and integration with swine manure wastewater treatment. The areal algal biomass productivity for the cultivation system that we developed ranged from 8.08 to 14.59 and 19.15-23.19 g/m(2) × day, based on ash-free dry weight and total suspended solid (TSS), respectively, which were higher than or comparable with those in literature. The harvested algal biomass had lipid content about 1.77-3.55%, which was relatively low, but could be converted to bio-oil via fast microwave-assisted pyrolysis system developed in our lab. The lipids in the harvested algal biomass had a significantly higher percentage of total unsaturated fatty acids than those grown in lab conditions, which may be attributed to the observed temperature and light fluctuations. The nutrient removal rate was highly correlated to the biomass productivity. The NH₃-N, TN, COD, and PO₄-P reduction rates for the north-located photo-bioreactor (PBR-N) in July were 2.65, 3.19, 7.21, and 0.067 g/m(2) × day, respectively, which were higher than those in other studies. The cultivation system had advantages of high mixotrophic growth rate, low operating cost, as well as reduced land footprint due to the stacked-tray bioreactor design used in the study.