The purpose of this study was to explore efficient methods of harvesting the microalga Phaeodactylum tricornutum. Natural sedimentation experiments, performed at different light and temperature conditions, did not yield significant improvements in efficiency even after 1 week. When alkalinity-induced flocculation was performed, both the flocculation efficiency and the concentration factor dramatically improved at pH = 9.75 (0.5–0.7 units over the original pH of the culture) after 10 min settling time. Sedimentation rates are documented at pH ranging between pH 9.75 and 11.0. The results of the application of two conventional flocculants used in wastewater treatment, polyaluminium chloride and aluminium sulphate, are also presented. Chitosan was also used as a natural flocculating agent to improve possible contamination problems in the downstream process. pH was adjusted in order to determine optimum flocculation efficiency of chitosan in combination with a high concentration factor. Satisfactory results were found with chitosan at an adjusted pH of 9.9 using concentrations as low as 20 mg L−1, after testing a flocculant range of 5–200 mg L−1.