Water leak

I noticed my bilge has kicked on every 5 minutes and shoots out water for a split second. I opened the battery box and noticed a small leak coming from the top port side motor mount bolt. But I doubted that it was the bolt itself. Today while cleaning the boat I noticed that the rub rail just above the bolt is missing about a 5 inch section. Could this be where my water is coming from? And yes the rub rail sits under the water. The boat is a 1992 Gambler.
Thanks in advance.

YES

How should I go about fixing this?

I bet there use to be a piece of plastic channel there.
To find leak shove a water hose in the live well drains and fill the live wells up,run the bilge,live well pumps ect.while it's on the trailer and look for hose leaks.
Then at night shine a bright light in the bilge and look for light on the transom.Or just silicon it up and put the plastic channel back.