Re: water in toon
I've owned 3 pontoons, one 1988 Manitou, one 1998 Tracker/Fisher/Spectrum, and one 2006 Forrester. All of them had drains at the rear and bottom of the tube, or drains were added by the dealer under warranty. I never had a drop of water in the Manitou logs. There was some water in the Forrester once that got in through the top side vent, when I left that plug out. I drained it out the drain holes, and haven't seen any since.
The selling dealer set my Tracker up wrong on the trailer and left about 2 feet of log hanging off the back. The boat had leaks at the top part of both tubes where the M brackets attach before it was 2 years old. A different dealer moved the boat up on the trailer and moved the axle to balance the load. He had a welder put drains in the rear of each log and weld about 2feet of the rear of each log at the M bracket. My cousin owns the boat now and as of last Saturday it has never had another drop of water in it. IMHO drain holes in pontoon logs are a very handy tool when needed, and about as big of a leak risk as the plug holes found on every conventional hull boat in the world. If my boat did not have them I would have them put in before I ever had a leak or water in a tube.
I would never try to test a pontoon by putting water in it. Quite often the leak is at the top of the log and the water gets in a drop at a time over months of use. If my Tracker logs had been filled to within 2 inches of the top the leaks would not have had water over them, and would not have been found. The proper method to test pontoon tubes is described in the FAQ section of the pontoon page. It is low pressure air in the vent or drain hole (under 5 PSI) and soapy water at the welds, seams, etc.
To the OP, you probably have vent plugs or tubes in the top of the logs. Water probably got in through those or through leaks at the rear of the tubes where they meet the deck (like mine did). Those are the places I have heard of water getting in most commonly. You might be able to pump it out through the vent holes using a vacuum pump or some other pump that will get down through that small hole and suck it up out. Eventually you will have to test the log or have it tested, then using whatever method you or your repairman feels is appropriate, drain the tubes, find the leaks and repair them.
Good luck and welcome to iboats.