This study attempted to determine an efficient flocculant that was used for the recovery of microalgal species, namely Scenedesmus. The biomass was grown in a pilot-scale raceway pond receiving domestic wastewater discharges. The microalgae achieved treatment efficiencies of 76.5% NH4+-N, 83.1% PO43−-P, 73.9% biological oxygen demand (BOD), and 42.8% chemical oxygen demand (COD). During microalgal harvesting, the highest biomass recoveries of 99.0%, 97.5%, and 96.5% were obtained by alum 300 mg/L at pH 7, chitosan 100 mg/L at pH 7, and cationic polymer 10 mg/L at pH 10, respectively. The protein, carbohydrate, and lipid yields of polymer-harvested biomass were 28.0%, 12.4%, and 17.4% (dry cell weight), respectively, which were higher than those obtained when applying either alum or chitosan flocculants. Moreover, the cationic polymer provided no detrimental effects on the fractions of fatty acids derived from the harvested microalgal cells. The microalgal biomass subjected to flocculation by either polymer or chitosan were entire and intact, whereas the lysis of cells was noticed during the alum flocculation process.