I'm not sure if this is even possible, but is there any way to gather ores and star fragments after they fall into the water? I just chased a star fragment literally forever and it landed on a cliff and dropped into a lake 😑
You currently can't dive in Zelda. So if something falls into the water and you can't pick it up while swimming over it you are out of luck.
The only solution how you interact with items below the water surface is the magnesis tool. So you can try to drop a magnetic weapon (or search for something magnetic) and try to "fish" with it, to push it to the beach and pick it up from there.
I created a cryonis slab near the underwater gems (but not TOO close or you can't see them or hit them), then used stasis on them one at a time and hit them with arrows to project them into shallower water so I could pick them up. A Lynel bow or Duplex bow works great because you get more hits with less arrows. Also you can pick up your arrows when you're done, as they float to the surface! Hope this helps!
Had this problem, diamond fell into a lake, what I did was stasis it and use arrows to hit it to shore. I tried to use magnesia and fish it out but it was very hard, I like this method better, it was how I did it. If it is too far use cryonis, bombs did not work for me though. Don't worry about your arrows, they will float back up (unless you are not using normal arrows or are using a x2, x3, or x5 bow).