Microalgae in three submerged ceramic membrane photobioreactors (SCMPBRs) with different hydraulic retention times (HRTs) were fed with permeate of a submerged ceramic membrane bioreactor for a period of 3 months to investigate the lipid content and also the biodiesel quality produced at different HRTs. The lipid content, lipid productivity and fatty acid compositions for all three SCMPBRs were not significantly different at the 95% confidence level. These results suggested that insigniﬁcant change in the amount of fatty acids was observed at different HRTs that supplied varying concentration of nitrate in the medium. Among the fatty acids, palmitic acid, palmitoleic acid, oleic acid and linoleic acid were the main components, whereas stearic acid was a minor fatty acid. Since there was insignificant effect of HRT on lipid content, lipid productivity and fatty acid compositions, the optimum HRT for SCMPBRs can then be designed based on optimum nutrient removal performance and low membrane fouling propensity.