First let me say I highly recommend using glass with glass and that it is cheaper and easier to work with. However, you can use acrylic if you do it properly and work with your limitations. It is more difficult, but in the end it will hold strong assuming you don't put a lot of pressure on it such as water on one side and no water on the other. If you are just building baffles or a weir, you will be in good shape with the tips below.
You will need to brace each corner and seam with a smaller run of acrylic. Basically you put in a panel and right next to it caulk in a 1" wide support that runs the length of the panel. If you need to suspend a panel such as in a bubble trap, you can do the same trick. You simply cut a 1"x1" block (assuming you have a 1" gap in your bubble trap) then rest the panel on the block so it can't slide down. Think of it as a mini shelf.
