Oyster reefs and their spatial patterns are deemed to change the local hydrodynamic condition and exert profound impacts on the grain size, concentration and transportation of suspended sediments. Meanwhile, high suspended sediment concentration often results in excess mortality among oysters. Oyster reefs are rare and vital ecosystem in Liyashan national marine park, Jiangsu Coast, China. However, urgent conservation efforts should be made on account of the drastic reduction in reef areas. To investigate the sediment dynamics and the geomorphology, two tripod observation systems were deployed and UAV aerial surveys with elevation measurement using Real Time Kinematic (RTK) were also carried out. High mud content (60％) was found in the bed sediment at the reef ridge, causing much lower drag coefficient than other recorded values of living oyster reefs, indicating the death of oysters and the degradation of reefs in Liyashan. Ridgelines of the string reefs at 45° to the current direction and high suspended sediment concentration in the water body (50–370 mg/L) that exceeds the threshold (200 mg/L), which would affect nutrient uptake efficiency and further result in gill saturation, decrease of clearance rate and associated deposition, were probably crucial causes of the death of oysters. The findings are useful for restoring natural oyster reefs and designing artificial reefs for nature-based coastal defense.