This isn't actually that hard, just requires you to alter your normal approach to solving things. If you use the magnet rune and look under the water there will be a fairly large bucket. Use this bucket and catch a ball inside of it. You can then transport the ball into the switch to unlock the gate.
The next part requires you to do the same. Rest the ball on top of the cage to the right. There is a roof on top of this one, but leave the ball there anyway. In the middle of the water is a red button. Drop the bucket you have been using onto this switch and it will make the ball fall onto the switch inside of the cage. You will now have the Daka Tuss Shrine puzzle completed.