We just got a 13 ft Boston Whaler with a 40 hp Johnson engine. Every time we get it to the ocean the engine doesn’t start. The plugs are flooded so we have to dry them and then it will start. Not what we are doing wrong. Should we be towing it with the engine flat or tilted up? We’ve been towing it with the engine tilt it up. Any thoughts??? Tia 

What year is the engine?

The first thing I would do is check the fuel.  If you are using pump gas, it most likely contains alcohol.  Alcohol attracts moisture.  You could have water in your fuel or a clogged fuel filter.  Drain all the fuel out of your engine, clean or replace the fuel filter, fill it with new gas and see what happens. 

If it’s a carbureted engine the floats are stuck open I see Glenn asked what year the engine is newer ones are fuel injected

 

You don’t wanna tow it with engine down you risk tearing up your Skeg and lower unit

There are probably a couple of issues going on.  First, it sounds like your float levels might be set a little too high.  Second, it sounds like you might be running a portable six gallon tank and towing it with the vent closed.  When towing it, the gas getting bounced around in the sun, it's building pressure in the tank and causing the needles in the carbs to push off the seats and some of the gas is getting into the engine.  Quick check/fix is to leave the gas hose off the engine until you get to the lake and open the vent before you connect it to the engine. 

Another thing you might be doing is over pumping the primer bulb and pushing the needles off the seat, causing it to flood the engine.  Try pumping it until you just start to feel a little pressure, don't squeeze it until it's hard. 

A weak spark or bad plugs can also cause plugs to wet foul extremely easily.  Make sure you have the recommended "Champion" Plugs in it.  Could be the wrong heat range.

Some of those earlier 40's had carburetors that were not that easy to adjust, it's very easy to get the low speed too rich on them and that will cause it to wet foul.