Load a tube of clear caulk into the caulking gun, and push the plunger forward until it fits snug against the back of the tube. Cut off the tip of the caulk's spout with a utility knife.
Stand inside of the greenhouse on a windy day. Holding your hand about an inch from the greenhouse wall, slowly move it along the seams between the panels of the greenhouse, feeling for an air current. Also look for any visibly damaged areas, or signs of water leakage.
Clean the surface of the damaged or drafty area, wiping away dirt and dust. Dry the surface, if necessary.
Push forward on the caulk gun's plunger to squeeze out a bead of caulk along the damaged area.
Push caulk bead into the crack or seam using the tip of your finger.
Repeat steps 1 through 5 until you have thoroughly checked and caulked the interior of the greenhouse.