The cheese industry produces substantial amounts of raw cheese whey wastewater (RW), which requires effective treatment prior to environmental disposal. This study presents an innovative sequential batch system that combines macrophyte and microalgal cultivation for RW remediation. The efficacy of Lemna minor MO23 in first-line photobioreactors (PBR-1) and Chlorella sp. MC18 (CH) or Scenedesmus sp. MJ23-R (SC) in second-line photobioreactors (PBR-2) for pollutant removal was evaluated. The nutrient removal capacity of L. minor, CH, and SC was assessed at optimal tolerance concentrations, alongside nutrient recovery from treated RW (TRW) by PBR-1 for microalgae biomass production. The results demonstrate that all three species effectively purified the cheese whey wastewater. L. minor efficiently removed COD, nitrate, phosphate, and sulfate from RW, producing TRW effluent suitable for microalgal growth. CH and SC further purified TRW, enhancing biomass production. CH outperformed SC with a 4.79% higher maximum specific growth rate and 20.95% higher biomass yield. Biochemical analyses revealed the potential of CH and SC biomass for applications such as biofuels and aquaculture. After treatment, the physicochemical parameters of the effluent were within the regulatory limits. This demonstrates that the PBR-1 and PBR-2 series-coupled system effectively purifies and recovers dairy effluents while complying with discharge standards.