Water flow LED Cube

gammerx:
I need help figuring out how this needs to be wired up

As far as I understand it, the decision of which LEDs to turn on when is unrelated to the hardware. The conventional solution that Crossroads describes gives you a matrix of LEDs each of which can be turned on and off fast enough for them to appear to be on continuously. Isn't that all you need? It is then up to you to decide which ones you want on when to get the effect you're after, but that's purely a software issue.