In this study, a 1200L outdoor pilot scale microalgal photobioreactor (PBR) was used for toilet wastewater (WW) treatment and evaluate its ability to remove pharmaceutically active compounds (PhACs). The PBR was operated at two different hydraulic retention times (HRTs), which were 8 and 12days, during Period I (September-October) and Period II (October-December), respectively. Algal biomass concentrations varied by operating period because of seasonal changes. Nutrients (ammonia, nitrogen and total phosphorous) and chemical oxygen demand (COD) were monitored and efficiently removed in both periods (>80%), attaining the legislation limits. At the theoretical hydraulic steady state in both periods, pharmaceutical removal reached high levels (>48%). Two harvesting techniques were applied to the PBR microalgae effluent. Gravity sedimentation was efficient for biomass removal (>99% in 7min) in Period I when large particles, flocs and aggregates were present. In contrast, a longer sedimentation time was required when biomass was mainly composed of single cells (88% clarification in a 24h in Period II). The second harvesting technique investigated was the co-pelletization of algal biomass with the ligninolytic fungus Trametes versicolor, attaining >98% clarification for Period II biomass once pellets were formed. The novel technology of co-pelletization enabled the complete harvesting of single algae cells from the liquid medium in a sustainable way, which benefits the subsequent use of both biomass and the clarified effluent.