My understanding is this:

A combo would be two skills that work well together. Using one with the other enhances your attack. A very basic example in DD, for example: you can use Curse to lower resists and then Elemental Strike to do more damage. It's not quite like lightning + water damage in your example, but I think it's the same idea.

Synergy would mean that simply enhancing a skill also enhances another skill. It's a passive system. I've never played Guild Wars, but look to Diablo II LOD post-1.10 patch to see what I'm talking about. +1 to blizzard enhances that attack, but also increases damage of your frost orb. (I think I made up that example, but that's how it works).

Feel free to correct me if I'm off the mark.