Acrylic would probably be a poor choice if you want the option of draining one side. Silicone caulk doesn't do well with plastics, having pressure on one side and not on the other is an invitation for it to fail. Unless the acrylic is thick enough to not bend under the pressure you would be adding additional pressure to the seal. If you are just looking at it as a divider to keep fish from getting through, or intend to keep the water depth the same on both sides all of the time it could work. 3m 5200 or other poly based caulks are supposedly better with plastics than silicone caulk, not sure if their bond is as strong as silicone caulk to plastic.
If you are just separating fish and not worried about separating the water (for lack of a better term) acrylic would be fine, or just get some hamburg matten foam and a couple of lift tubes and turn the divider into a filter.