Nanosized iron (hydr)oxides and phosphate minerals are widely distributed in supergene environments and exhibit significant sequestration effects for phosphorus (P) and Rare Earth Element (REE). Although previous studies have found that both forms of P can be utilized by microorganisms, the mechanism by which microbial activity constrains the geochemical behavior of mineral-bound REEs during P utilization has received little attention. This study investigated the utilization of Nano-mineral bound P by Microcystis aeruginosa and the associated REEs fractionation under weakly alkaline and high CO {}_{\mathrm{3}}^{\mathrm{2}-} conditions, using ferrihydrite (Fh) and apatite (Ap) loaded with P and REEs as P sources through dialysis methods (isolating cells from minerals). The results demonstrated that M. aeruginosa utilized nano-mineral-bound P with low efficiency, while both dissolved and nano-mineral-bound REEs exhibited moderate toxicity to the cyanobacterium. In the REE experiments, all the solutions were enriched in Heavy REEs (HREEs) after 17 d of cultivation. For algal cells and Extracellular Polymeric Substances (EPS), REE fractionation was observed only in experiments with high dissolved REE concentrations (enriched in LREEs and LREEs) and ferrihydrite + dialysis (enriched in HREEs). Filamentous EPS preferentially accumulated middle REEs (MREEs, particularly Sm, Eu, and Gd), whereas secondary calcium phosphates and iron (hydr)oxides sequestered MREEs-HREEs. It is considered that: ① Selective adsorption of REE³⁺ under weak alkaline conditions by Cells and EPS (C&E) consistently enriches HREEs in solutions; ② Cells and EPS enrichment in LREEs occurs when the REE/anion (especially CO {}_{\mathrm{3}}^{\mathrm{2}-}) ratio in solution is elevated; ③ No REE fractionation in cells and EPS when REEs originate from mineral phases; ④ EPS-mediated selective REE complexation from minerals may drive HREE enrichment in cells and EPS; ⑤ Preferential accumulation of MREEs-HREEs in EPS and secondary solid phases may underlie the positive anomalies of these elements in eutrophic waters. Thus, anomalies in MREEs (e.g., Eu) may serve as effective proxies for assessing the degree of aquatic eutrophication.