I had my batteries on a full charge this last weekend while fishing, but my trolling motor went out after about two hours on the water. Any suggestions on what i should do, as i have no electrical or mehanical knowledge to speak of. Just a general place to start would be greatly appreciated. It is only 2 yrs old as well.

Have the batteries tested

Bad battery or two! That's where I'd start.

I would start by having the batteries checked to make sure there good

Make sure that the batteries are wired correctly for your application. Series (24v)or parallel(12v)

Before you get them tested you need to make sure they are properly connected in the right sequence. Next thing is to make sure all connections are tight and corrosion free. If that all checks out then you probably do have a need to have the batteries checked out. It sounds like you have a dead cell. Make sure you have them tested by someone who knows how to properly test them. It is possible your charger is faulty also. Last but not least is the possibility that your wiring harness going from the batteries to the trolling motor or the plug has a problem such as a significant resistance or faulty connection.

I had mine checked once and the guy said nothing was wrong. They were only one year old and I insisted that they would go flat in 2-3 hrs. so he replaced both of them. Problem solved. what I'm saying is that I had a battery problem that didn't show up when tested but after replacing them I had no more problems.

Yes, agree with everyone. Almost 100 percent a battery or wiring issue.

Battery. But as said check all your connections. And don't forget the connection that the leads connect to on the panel that goes to the front of the boat if you have one.That one fooled me once.

After you check your wiring and you still have issues buy a cheap voltage meter from Harbor Freight, you should be reading between 12 and 13 volts after charged. If less than that you have a bad battery.

A cheap little voltmeter is your friend. You can check voltage at full then see which batteries are puking on themselves as you unload. Bad ones drop fast. I get a little more that 13 when full. My 36 volt system will read 40 and change on full charge. They are all kinds of handy to have in the boat.

I had a very similar issue on my 24volt system. After trying everything I could think of,and then fishing a tournament without my bow mount working I was embarased to find "one" of the "two" fuses in my (factory)system had burnt out. I suspect it happened when I had my prop jammed in sticks.