Seabed particles with low shear stress limits are prone to erosion and sedimentation, affecting the balance of aquatic ecosystems. The water flow velocity triggered by the rotation of the ship's propellers can reach the seabed and exert significant pressure on elementary particles. However, by setting the propeller rotation threshold, the process of erosion and sedimentation of the seabed can be controlled. This study determines the propeller rotation threshold of the Landing Craft Tank (LCT) ship based on the water flow velocity it produces. The water flow velocity was investigated at several variations of propeller rotation (rpm) and variations of water depth using numerical and empirical approaches. Then, scale model experiments were carried out in the laboratory. Analysis based on the general standard criteria for erosion and sedimentation shows that an LCT vessel with a propeller diameter of 1.5 meters can use a propeller rotation of 25 rpm in all water depths. The propeller rotation of 75 rpm is safe if the propeller shaft distance to the seabed is at least 1Dp (Dp is the propeller's diameter). A 120 rpm propeller rotation is safe to use at a minimum distance of 1.5Dp, and a 230 rpm propeller rotation is safe for a minimum distance of 2Dp. Threshold values vary based on the particle type and the water depth. The propeller rotation threshold criteria are essential in determining the new under-keel clearance (UKC) to realize environmentally friendly ship operations.