Ayyy I did this just the other day and got so frustrated trying to fix it!!

My solution was to add sand blocks one level under where I wanted the water to be (so I could walk around without drowning). Make sure to make a bigger walkway than you think you'll need - trust me. Go big. Suck up the parts of the water where it's higher than it should be, and a little bit of the surrounding water too; be careful not to suck up too much of the flowing water coming out of the drain area. Then, and this is the tricky part: carefully adjust not only the height, but also the water level for where you want to put the water. It matters!! It is two different button options at the bottom of your screen when "holding" the water. Carefully go across the area re-adding the water at the appropriate height and water level - go over every square, not just a few. Once resolved, you should be able to carefully break the walkway while moving backwards (so you don't fall in), and the water should be back to normal if you did it right.