There are multiple methods to repair leaking rivets on an aluminum jon boat. Some are mechanical, involving resetting the rivets; some are chemical, using a sealant around the rivets. All the methods have one thing in common: Before you begin the repair, you fill the boat with water, to find the leaks.
Mechanical Repair
Fill the boat with water. Mark the leaking rivets, and have a friend stand inside the boat that’s still filled with water, with a large hammer. Tell your friend to hold the hammer to the head of each leaking rivet – inside the boat -- in turn. Place the butt of a piece of 3/4-inch rebar against the tail of the leaking rivet, outside the boat. Strike the opposite end of the rebar with a hammer until the rivet tightens up and the leak stops. When the leaks stop, drain the water from the boat. Never use a drill to remove a rivet that won’t tighten up. Instead, chisel the head of the rivet off with a wood chisel and replace the rivet.
Chemical Sealing
Fill the boat with water and mark any leaking rivets. Empty the boat. Mix the hardener and resin of an epoxy sealing compound, such as West System's GFlex 650, according to the compound's directions. Heat the seamed area and rivets with a propane torch to dry the seam. Apply the epoxy compound to the seam by painting the compound onto the seam with a plastic paint scraper or by injecting the epoxy into the seam with a specialized syringe. After filling the seam, heat it with a heat gun until the epoxy sets.