To meet the increasing demand of high-quality microalgae for use as feed for aquaculture, development of more cost-effective and sustainable microalgal production facilities is needed. In shellfish hatcheries, algae are currently mainly cultivated in plastic bags, which have a relatively small capacity and require high labor costs. Fully-automated closed photobioreactors (PBRs) have been proposed as most-promising alternative method for producing these algae. A lot of the microalgae used in hatcheries are found to be sensitive to hydrodynamic forces. PBRs should therefore be equipped with recirculation pumps that do not damage the algae. Ways to make the production more economically and ecologically sustainable are the use of sunlight instead of artificial light. If sunlight is used, the productivity in PBRs can be improved by tuning the biomass concentration with the different light conditions over the year. This study showed that the production can also be made more economically and ecologically sustainable by turning off the temperature control at night and by cultivating microalgae on wastewater from fish farms. The wastewater not only provides free nutrients for the production of microalgae as feed for shellfish, but also enables re-use of the purified water.