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Taxa-specific responses to the increasing anthropogenic eutrophication offer promising insights for mitigating harmful algal blooms (HABs) in freshwaters. The present study evaluated the HABs species dynamics in response to the ecosystem anthropogenic enrichment during cyanobacterial-dominated spring HABs in the Pengxi River, Three Gorges Reservoir, China. Results show significant cyanobacterial dominance with a relative abundance (RA = 76.54 %). The ecosystem enrichments triggered shifts in the HABs community structure from Anabaena to Chroococcus , especially in the culture involving iron (Fe) addition (RA = 66.16 %). While P-alone enrichment caused a dramatic increase in the aggregate cell density (2.45 × 108 cells L−1), the multiple enrichment (NPFe) led to maximum biomass production (as chl- a = 39.62 ± 2.33 μgL−1), indicating that nutrient in conjunction with the HABs taxonomic characteristics e.g., tendency to possess high cell pigment contents rather than cell density can potentially determine massive biomass accumulations during HABs. The stimulation of growth as biomass production demonstrated by both P-alone and the multiple enrichments, NPFe indicates that although P exclusive control is feasible in the Pengxi ecosystem, it can only guarantee a short-term reduction in HABs magnitude and duration, thus a lasting HABs mitigation measure must consider a policy recommendation involving multiple nutrient management, especially N and P dual control strategy. The present study would adequately complement the concerted effort in developing a rational predictive framework for freshwater eutrophication management and HABs mitigations in the TGR and elsewhere with similar anthropogenic stressors. [Display omitted] • Nutrient responses on HABs' growth in the Pengxi River indicate primary limitation by P. • HABs community structure demonstrated a significant ecosystem cyanobacterial dominance. • Nutrient enrichment, especially Fe triggered a dynamic shift from Anabaena sp. to Chroococcus sp. • Toxin production across the enrichments was controlled by dinoflagellate despite cyanobacteria dominance. [ABSTRACT FROM AUTHOR]