Microalgal-indigenous bacterial wastewater treatment (MBWT) emerges as a promising approach for the concurrent removal of nitrogen (N) and phosphorus (P). Despite its potential, the prevalent use of MBWT in batch systems limits its broader application. Furthermore, the success of MBWT critically depends on the stable self-adaptation and synergistic interactions between microalgae and indigenous bacteria, yet the underlying biological mechanisms are not fully understood. Here we explore the viability and microbial dynamics of a continuous flow microalgae-indigenous bacteria advanced wastewater treatment system (CFMBAWTS) in processing actual secondary effluent, with a focus on varying hydraulic retention times (HRTs). The research highlights a stable, mutually beneficial relationship between indigenous bacteria and microalgae. Microalgae and indigenous bacteria can create an optimal environment for each other by providing essential cofactors (like iron, vitamins, and indole-3-acetic acid), oxygen, dissolved organic matter, and tryptophan. This collaboration leads to effective microbial growth, enhanced N and P removal, and energy generation. The study also uncovers crucial metabolic pathways, functional genes, and patterns of microbial succession. Significantly, the effluent NH₄⁺-N and P levels complied with the Chinese national Class-II, Class-V, Class-IA, and Class-IB wastewater discharge standards when the HRT was reduced from 15 to 6 h. Optimal results, including the highest rates of CO₂ fixation (1.23 g L^-1), total energy yield (32.35 kJ L^-1), and the maximal lipid (33.91%) and carbohydrate (41.91%) content, were observed at an HRT of 15 h. Overall, this study not only confirms the feasibility of CFMBAWTS but also lays a crucial foundation for enhancing our understanding of this technology and propelling its practical application in wastewater treatment plants.

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