<p>Environmental DNA (eDNA) detection in aquatic systems is influenced by multiple environmental factors that can be broadly classified into physical and biological processes. Physical factors include water flow, turbidity, and ultraviolet radiation, whereas biological factors include microbial activity that promotes DNA degradation. River dynamics, which are often disrupted by flooding and flow events, can affect eDNA detection. The increased flow during floods and sediment drift cause turbidity. The effects of sediment drift on eDNA, including adsorption, degradation, and PCR inhibition, and the effects of flow on eDNA, including dilution, have been previously studied. However, the combined effects of flow and sediments on eDNA detection have not been extensively explored. In the present study, we investigated the influence of flow and sediment on eDNA concentrations in closed-bottle aquariums with zebrafish to distinguish the effects of these physical forces from those of eDNA dilution. Our results revealed that flow affects eDNA concentration not only through dilution, but also through physical destruction, indicating that fast flows can physically degrade eDNA. Additionally, the effects of sediment on eDNA varied with the presence of flow. The eDNA settled in the sediment and could potentially be preserved without flow. However, in the presence of flow, sediment particles caused physical damage to suspended eDNA, thereby accelerating its eDNA degradation. This study represents a first step toward understanding eDNA degradation behavior during floods while considering sediment drift.</p>