Apply masking tape on both sides of the original caulking, leaving a 1/4-inch width between them.
Lay down a 1/4-inch bead of caulk between the tape. Depress the caulking gun trigger to release the caulk.
Smooth out the caulk with the bottom of a spoon. This gives the caulk a finished appearance.
Remove the masking tape immediately. Do not let the tape sit or the caulk will cure on it and you will not be able to remove it.
Assess the damage to the sill. If the water damage extends more than 1/4 inch into the wood, you will need to replace the entire sill. If not, you can repair this on your own.
Sand down the window sill with a hand sander. Do not start the sander when it is in contact with the wood or it will gouge the surface. Hold it up, turn it on low and lower it slowly on to the wood. Sand the entire sill until the damaged area has been removed.
Sand the surface again with a fine-grit sanding block. This will prepare the wood for refinishing.
Stain or paint and prime the wood. If staining the wood, apply one coat of stain and let it dry for four hours. If the desired color has been reached, proceed to the finishing stage. If not, apply another coat and let it dry. If painting the wood, prime the surface first and let the primer dry. Apply at least one coat of paint to the wood.
Seal the wood with a clear polyurethane sealer. This will help prevent future water damage. Paint on one coat of sealant and let it dry.