My first two demos (Waveride and Armitage by Straylight if you search on Pouet) used a 3-array water surface simulation, cycling through them like you mentioned. The first used an implementation on the CPU with a 128x128 grid, the second did 5 separate 128x128 surfaces on the GPU (render to texture). The second ran all 5 about 10x faster than running a single one on the CPU, and that was with effectively no optimization on the GPU side. With some tweaking, I would've been able to do 10000^2 grids cheaply; the biggest bottleneck was that I moved the textures to and from the GPU for each frame, which I could eliminate with some use of vertex shaders and abuses therein.

Anyway, saying that GPGPU is overkill here is pretty silly -- sure, you can do some water surface simulation on the CPU, but you hit the wall very, very quickly if you're doing anything but that.