tiny voices :
You will need a way to completely isolate the water form the wood. Like a plastic insert instead of the window.
Yes, the water will not come out of the wood. I'm going to say glass for now but something else will most definitely be used. Basically, the window (actually I should say side panel, because it will span the height and width) is detachable and slides into grooves on the wood. You can fill the water by detaching the side panel and filling water and dye into it. Then, insert the plug so the water does not leak, and slide it back into the grooves and then you have your water side panel.
The sliding is also very easy in terms of installing your parts. Need to edit a part? Just slide out the side panel, make some modifications, slide it back in.