Global increase in aquaculture production has created a need to reduce its environmental impacts. Nutrients could be recycled especially at land-based recirculating aquaculture systems (RAS) by cultivating green microalgae in aquaculture effluent. However, microalgae are difficult to harvest. As a multi-trophic solution, mussels could be used in harvesting microalgae. We tested three European freshwater mussels (duck mussel Anodonta anatina, swan mussel A. cygnea, and swollen river mussel Unio tumidus) for filtering two common green microalgae (Monoraphidium griffithii and Selenastrum sp.) grown in RAS effluent. Mussels decreased microalgal concentrations in the tanks 42–83% over three consecutive trials. Algal concentrations at the end of each trial were lowest for both microalgae in tanks containing Anodonta mussels. Clearance rates were higher for Anodonta mussels than for U. tumidus. Mussels biodeposited more microalgae to tank bottoms when M. griffithii was filtered. Ammonium concentration decreased or did not change in tanks with M. griffithii, but increased in tanks containing Selenastrum sp. These results suggest that of the tested species Anodonta mussels and M. griffithii show best potential for RAS effluent bioremediation application. We conclude that a co-culture of microalgae and unionid mussels could be used for recycling nutrients in aquaculture.