A common mistake that many boat owners make is trying to seal leaking boat ports and windows in the same way they would seal a leaking house window. If you run a bead of caulk around the frame, it will only temporarily solve the problem. Caulk that hardens in the sun will crack and leak again when the body of the boat flexes under strain. Leaking boat ports and windows must be removed and a new sealing bed of caulk installed to fix this problem correctly.
Release the tension of the frame-mounting screws of the port or window by using a flathead screwdriver to turn them in a counterclockwise direction. Some boats may have an additional Fiberglas or rubber covering placed over the frame to hide the screws. Gently ply that covering off and then release the tension. You do not want to remove the screws completely. Just release the tension holding the frame into the body of the boat so the port or window feels loose.
Scrape out the old caulk from around the frame on both the inside and outside of the leaking boat port or window. Be careful not to scratch into the finish on the boat's hull.
Release more tension off the frame-mounting screws until you can lift the entire port or window out of the body of the boat.
Scrape all the old caulk from the frame and from the hole in the boat's body. You want both surfaces to be clean.
Load your caulk into your caulk gun, according to the instructions of your model caulk gun. Apply a bead of caulk all around the boat port or window in the centre of the frame.
Set the port or window back into place in the boat's body. Use wood shims to hold it in place.
Caulk all around the frame of the port, from the inside and the out, making sure that the caulk is going into the space between the port or window frame and the body of the boat. This creates the new sealing bed for the window.
Tighten the frame tension screws. As you feel the frame begin to set into place, pull your wood shims out. Continue tightening until you see a thin bead of caulk begin to press out around the edge of the frame. Trim this off with your putty knife and allow the caulk to set, according to the time specified on the package, before using your boat.
Plan your work at low tide so that you do not have to remove the boat from the water to perform this repair.
Never use a caulk that is not clearly marked as "marine grade" to perform any leak repairs on a boat. Other types of caulk will remain water resistant for only a short while. After that, they will fail, causing extensive water damage to the interior of your boat.