Given its high biomass production, phytoremediation capacity and suitability as a feedstock for animal and human nutrition, duckweeds are valuable multipurpose plants that can underpin circular economy applications. In recent years, the use of duckweeds to mitigate environmental pollution and valorise wastewaters through the removal of excess nitrogen and phosphate from wastewaters has gained considerable scientific attention. However, quantitative data on optimisation of duckweed performance in phytoremediation systems remain scant. In particular, a mechanistical understanding of how physical flows affect duckweed growth and remediation capacity within vertical indoor multi-tiered bioreactors is unknown. Here, effects of flow rate (0.5, 1.5 or 3.0 L min−1) and medium depth (25 mm or 50 mm) on Lemna minor biomass production and phytoremediation capacity were investigated. Results show that flow rates and water depths significantly affect both parameters. L. minor grew best at 1.5 L min−1 maintained at 50 mm, corresponding to a flow velocity of 0.0012 m s−1. The data are interpreted to mean that flow velocities should be low enough not to physically disturb duckweed but still allow for adequate nutrient mixing. The data presented will considerably advance the optimisation of large-scale indoor (multi-tiered, stacked), as well as outdoor (pond, lagoon, canal), duckweed-based remediation of high nutrient wastewaters.