Filamentous fungi can be used to form easily harvested pellets with microalgae (fungal-assisted algal harvesting) in order to advance the sustainability and economic feasibility of wastewater treatment using microalgae. In experiments employing the microalga Chlorella vulgaris and using the filamentous fungus Aspergillus niger for harvesting, this study investigated the effect on water quality and the quantity and quality of lipids in the biomass produced. Major reductions in the concentrations of total nitrogen, ammonium-nitrogen and total phosphorus were observed after addition of the fungal spores (day 5) and during fungal growth and entrapment of the algal cells. At harvest (day 8), the decrease in total nitrogen was 47.4% ± 18.4% of the initial value, corresponding to a reduction of 41.9 ± 17.1 mg•nitrogen•L −1. For total phosphorus, the decrease was 94.4% ± 3.2%, corresponding to a reduction of 6.4 ± 0.2 mg•phosphorus•L −1. A significant decrease in concentration of the micropollutant diclofenac was observed at harvest, to 5.1 ± 4.0 µg•L −1 compared with an initial concentration of 9.5 ± 0.6 µg•L −1. A significant decrease in total lipids in the biomass was observed after fungal-assisted algal harvesting, from 58.7 ± 2.7 µg•mg −1 at day 5 (algal biomass only) to 34.2 ± 2.7 µg•mg −1 at day 8 (fungal-algal biomass). However, because of high biomass production, the amount of lipids produced per litre of wastewater increased from 5.6 ± 0.9 mg on day 5 to 20.6 ± 4.9 mg on day 8.