Abstract: Aggregation is a basic unit to form sediment structure. The structure of sediments impacts on the stability, infiltration and strength of engineering geologic properties. A study was implemented in the abandoned riverway of Yellow River Estuary, Diaokou, on the influence of clay, organic matter and biologic EPS (extracellular polymeric substances) on the aggregation. The results indicate that the sediments mainly become 0.05~0.01 mm aggregation. The content of the aggregation is between 85.3% and 95.8%. Compared with loess in loess plateau, the aggregation of 0.05~0.01 mm increases,and that of 0.1~0.05 mm decreases. The aggregate stability is poor so the sediments are easier to erode. The clay content is in positive correlation with aggregate ratio,which indicates the more the clay content the more stable the aggregation. The mineral composition is not good to aggregate stability. The content of organic matter is between 0.27% and 0.61%. The influence of organic matter on sediment aggregation is little. The aggregation ratio from the sediment of crab cave and crab dug is more than that of the surface sediment without bioturbation. This indicates that the EPS produced by crab can increase the aggregation stability.