Abstract Diatoms are the major group of microalgae which have been utilized by the potential applications as food industries, aquatic feeds, cosmetics, biofuels, and pharmaceuticals. In this study, current approaches were made in order to determine growth rate, biomass productivity, protein, carbohydrate, lipid and fatty acid composition for Nanofrustulum shiloi cultures using both aeration and mixing conditions in flat-plate photobioreactor (PBR). Physical (the intensity of aeration, mixing, light intensity etc.) and chemical (nutritional materials) factors are affecting the growth and bioproduct contents of a diatom. Biomass and lipid productivities of N. shiloi were measured as 31.29 and 36.9622±0.0598 mg L-1 day-1 in flat-plate PBR having the combination of aeration and stirring system, respectively. A slightly higher amount of saturated fatty acids was detected in PBR having only bubbling system while the increase of mono- and poly- unsaturated fatty acids were found in PBR having the combination of aeration and stirring system. Flat-plate PBR design was also investigated for improving not only biomass but also the lipid productivity of N. shiloi.