A compressible boot seal for sealing the side of a vertical traveling water screen with flights. The boot seal is formed by a U-shaped, bent nylon plate having a bottom base that resides in the boot section at the lower end of the traveling water screen and two upwardly extending arms that are attached at their distal ends to a side of the water screen support. The plate is bent at the intersection of the base and the arms to form a living hinge that allows the plate to deflect toward the side of the support on contact with side edges of the flights. The hinge seals the plate against the side edges of the flights. A resilient filler material fills the void between the plate and the side of the support to prevent sand and debris from interfering with the deflection of the side seal.