Recent research has demonstrated the potential of using filamentous fungi to form pellets with microalgae (biopellets), in order to facilitate harvesting of microalgae from water following algae-based treatment of wastewater. In parallel, there is a need to develop techniques for removing organic pollutants such as pesticides and pharmaceuticals from wastewater. In experiments using the microalga Chlorella vulgaris , the filamentous fungus Aspergillus niger and biopellets composed of these microorganisms, this study investigated whether fungal-assisted algal harvesting can also remove pesticides from contaminated water. A mixture of 38 pesticides was tested and the concentrations of 17 of these were found to be reduced significantly in the biopellet treatment, compared with the control. After harvesting, the concentration of total pesticides in the algal treatment did not differ significantly from that in the control. However, in the fungal treatment and biopellet treatment, the concentration was significantly lower (59.6 ± 2.0 µg/L and 56.1 ± 2.8 µg/L, respectively) than in the control (66.6 ± 1.0 µg/L). Thus fungal-assisted algal harvesting through biopellet formation can also provide scope for removing organic pollutants from wastewater, with removal mainly being performed by the fungus.