Water basically has a counter for everything, if you know what your foes are, so it's well suited to a variety of challenges. But if your debuffs miss, things can get ugly quickly. Also, there will be an ATK debuff cap of -50% soon. Without Cthulhu and Snow Raphael, who provide a means to counter overdrives without relying purely on ATK down cheese, Water teams relying on utility SRs will struggle in top difficulty content.
I don't think I can handle Thunder with my Water team yet, not without powered-up accessories at least. Maybe if I had a perfect team. But I don't really need to. I just need to clear Water quests (namely, the final boss) all the time, and the others most of the time to progress at an optimal rate.