Scour caused by a water jet impinging the bed-sediment layer is a significant concern for hydraulic engineers. Although several studies investigated the maximum scour depth on the non-cohesive bed-sediment layer, the effect of the bed-sediment layer's thickness on the scour was not studied. This study investigated the effect of the thickness of the non-cohesive sediment layer at the canal bed on the depth of the scour caused by a water jet. The dimensionless parameters affecting the depth of the scour were obtained via dimensional analysis. Experiments were conducted on two different, non-cohesive bed-sediment layers at the bottom of a rectangular canal for different jet Froude numbers. Experimental results indicated that the depth of the scour increases with the thickness of the bed-sediment layer; this is because as the thickness of the sediment layer increases, the penetration depth of the air bubbles (dragged and enforced by the impinging water jet) through the sediment layer just under the scour hole increases. Due to the buoyancy force, as the air bubbles rise upward, they apply uplift forces and dynamic effects onto sediment particles, dislodging, suspending, and carrying the sediment particles away from the bed. If the thickness of the sediment layer is increased beyond a limiting value for a given flow condition, the maximum depth of the scour does not change (it remains almost constant). The effect of the thickness of the bed-sediment layer on the depth of the scour is present but not excessively large.