Piecemeal armor rules say plate arms have an armor penalty of -7, and that when combining multiple pieces you take the worst armor penalty, and that a suit of full plate includes the plate arms. Thus I'm confused about why the armor penalty for a full set is only -6, and not -7.
Fortification is a magical enhancement.
This suit of armor or shield produces a magical force that protects vital areas of the wearer more effectively. When a critical hit or sneak attack is scored on the wearer, there is a chance that the critical hit or sneak attack is negated and damage is instead rolled normally.
Fortification Type Chance for Normal Damage Light 25% Moderate 75% Heavy 100%
The base armor could be any type. It needs to be magic armor, ie, have at least a +1 bonus.
In addition to an enhancement bonus, armor may have special abilities. Special abilities usually count as additional bonuses for determining the market value of an item, but do not improve AC. A suit of armor cannot have an effective bonus (enhancement plus special ability bonus equivalents) higher than +10. A suit of armor with a special ability must have at least a +1 enhancement bonus.
You'll need to ask your DM for more details on your specific armour.
The Rules Don't Say
As nvoigt pointed out, the PHB describes chain mail and plate mail as complete items. They are either on, or they're off. There are rules for how long it takes to put them on and take them off, but there is no description for your AC while wearing just the padding.
Furthermore, the padding under plate and chainmail isn't padded armor. Padded armor is a different thing. When you buy plate mail you don't get plate mail armor that has padded armor inside, you get plate mail armor that has padding inside.
You Could Try It
Since there are no rules that describe this situation, you are down to the most general rule of all. At the beginning of the Players Handbook, it says:
1.The DM describes the environment. ... 2.The players describe what they want to do. ... 3.The DM narrates the results of the adventurers' actions. (PHB p.6, "How to Play")
So, your character could just try it and see what happens. "Try it" could mean a lot of things. "My character takes off all his armor but the padding. What's his AC?". "I'm looking at the swamp we're about to cross. I'm an experienced fighter, I've been wearing armor for years, I've been trained by experts. I know if I fall in wearing full plate, I'll probably drown before I can get out of it. What does my training tell me about whether I can wear just the padding in order to mitigate the drowning risk but still retain some protection?" Or perhaps your armor wearer might consult armor experts.
You've Solved My Drowning-in-Armor Puzzle!
As a GM, I view the water-armor situation as a challenge or problem for the PCs. Which do you do, take off the armor and carry it thereby lowering your AC, or wear it and risk drowning?
Only it isn't an either-or, which is the beauty of RPGs. There are other solutions to the problem. Perhaps the water is such and the PC's strength is such that the PC can just walk out, perhaps with a strength or constitution check. Perhaps the PCs have access to magic that allows them to breathe water. Maybe they can bypass the swamp. The players might (and hopefully will!) have innovative solutions I haven't thought of.
If the PC said, "I take off most of my armor, and wear only the padding", or "only the helmet, gauntlets, greaves and leg guards" and subsequently fell into the water I think the time to remove the armor and thus the risk of drowning would be less, while the chances of swimming in part of the armor would be more. And if the PC were attacked by Rodents of Unusual Size while crossing the swamp, I'd definitely have to allow that the PC's base AC in padding or other bits and pieces was greater than without armor. Wearing only part of the armor might be a reasonable solution to the but-I-might-drown problem. Although wearing only the padding might be really bad for it, given briars and such.
Given that I don't want to play "Armor & Anoxia" I'd be reluctant to come up with a codified houserule that says you can wear half the armor for half the AC and half the risk of drowning, but perhaps that would be the solution. I'd definitely want to keep things liquid, and not weigh the game down with heavy armor questions, but I'd definitely want to pad it enough to keep things moving forward, while at the same time rewarding innovative role-play and problem-solving.