To determine the cause of the population decline in Gobiobotia naktongensis, substrate preference and burying behaviour were investigated in this study. In general, the species was shown to prefer a substrate size of 1 mm or less, depending on the flow. In addition, the burying depth varied according to the size of the fish and increased with a decrease in water temperature. Our findings showed that the main cause of the population reduction was the physical changes in the substrate structure due to the dams or barrages construction. Notably, the accumulation of silt and mud in the substrate upon the formation of an upstream lentic water region for structural construction and bed armouring caused by scouring and reduced downstream inflow of fine sediment were deterministic in the fish habitat changes, causing problems in burying. As sand substrate structure is critical for the survival and inhabitation of psammophilous species, efficient strategies should be developed with proper habitat management to reduce the anthropogenic damage