Suspended sediment transport in coastal estuaries is profoundly shaped by microbial activities, yet the underlying molecular mechanisms remain poorly constrained during their flocculation. Here, we demonstrate that the estuarine bacterium <em>Stutzerimonas decontaminans</em> acts as a key mediator of sediment flocculation. Compared to purely physical aggregation, microbially-induced flocculation developed more slowly but yielded flocs fourfold larger, with looser fractal structures and higher organic carbon content, indicating strong microbial-mineral coupling. Bacteria modulated flocculation both physically via flagella-driven adhesion and biochemically through extracellular polymeric substances, which enhanced particulate organic carbon accumulation. Transcriptomic analyses revealed an early upregulation of flagellar genes initiating particle adhesion, followed by the activation of polysaccharide biosynthesis pathways to stabilize aggregates. This sequential regulation highlights a genetic trade-off between motility and biofilm-like stickiness in controlling floc growth. Our findings provide direct molecular and structural evidence that microbial activities fundamentally reshape sediment aggregation dynamics, thereby regulating suspended sediment transport and carbon cycling in coastal systems.