Suspended particulate matter (SPM) and biofilm are critical in removing contaminants in aquatic environments, but the environmental behavior and ecological toxicity of SPM-biofilm aggregates modulated by turbulence intensities are largely unknown. This study determined the removal pathways of microcystin-LR (MC-LR) by SPM and its biofilm under different turbulence intensities (2.25 × 10–3, 1.01 × 10–2, and 1.80 × 10–2 m2/s3). Then, we evaluated the toxicity of SPM-biofilm aggregates to Daphnia magna. The results revealed that SPM contributed to the adsorption of MC-LR, and the removal of MC-LR can be accelerated with biofilm formation on SPM, with 95.66 % to 97.45 % reduction in MC-LR concentration under the studied turbulence intensities. Higher turbulence intensity triggered more frequent contact of SPM and MC-LR, formed compact but smaller clusters of SPM-biofilm aggregates, and enhanced the abundance of mlrA and mlrB; thus benefiting the adsorption, biosorption, and biodegradation of MC-LR. Furthermore, the SPM-biofilm aggregates formed in turbulent water triggered oxidative stress to Daphnia magna, while a weak lethal toxic effect was identified under moderate turbulence intensity. The results indicate that the toxicity of SPM-biofilm aggregates fail to display a linear relationship with turbulence intensity. These findings offer new perspectives on understanding the environmental behavior and ecological outcomes of SPM and its biofilms in turbulent aquatic environments.