This is unfortunately going to be a roundabout solution that requires a little work, but the best way to fix this would be to upgrade your ship.
Based on your screenshot, you've still got the tier 1 space ship, which has the pilot's seat area, a small amount of storage space, and the teleporter. If you upgrade to the second tier, a new room will be added behind the teleporter. Remove the barricade from the new room, and the water should flow in (and probably disappear since it doesn't look like there's enough there to cover the floor of the new room).
To upgrade your ship, you need to either recruit two crew members (by doing quests for NPCs in any town, who will then occasionally decide to join you) or you can buy the "Fake Kestral License" from the Penguin Bay, then bring the license to Pete (far right in the Outpost). It does require a handful of upgrade modules (which are pretty common).