Cyanobacteria and microalgae are considered as interesting feedstocks for either the production of high value bio-based compounds and biofuels or wastewater treatment. Nevertheless, the high costs of production, mainly due to the harvesting process, hamper a wide commercialization of industrial cyanobacteria and microalgae based products. Recent studies have found in autoflocculation and bioflocculation promising spontaneous processes for a low-cost and environmentally sustainable cyanobacteria and microalgae biomass harvesting process. In the present work, bioflocculation process has been studied for three different inocula: filamentous cyanobacteria, microalgae and their mixture. Their cultivation has been conducted in batch mode using two different cultivation media: synthetic aqueous solution and urban wastewater. The removal of nutrients and flocculation process performance were monitored during the entire cultivation time. Results have proved that bioflocculation and sedimentation processes occur efficiently for filamentous cyanobacteria cultivated in synthetic aqueous solution, whereas such processes are less efficient in urban wastewater due to the specific characteristics of this medium that prevent bioflocculation to occur. Besides different efficiencies associated to cultivation media, this work highlighted that bioflocculation of sole microalgae is not as effective as when they are cultivated together with filamentous cyanobacteria.