I think part of the problem is GEGL updating the display as the parameters are adjusted.
I wonder if this works for you
Select a small representative area of the larger image.
Edit -> Paste as a new Image
Apply water pixels to that small image, with your settings
Back to the large image and use Filters -> Repeat Last to the image.
The display is not updated until the filter is complete
This with a 4896 x 3264 photo https://i.imgur.com/yn2DaEZ.mp4
might work.
I wonder if this works for you
Select a small representative area of the larger image.
Edit -> Paste as a new Image
Apply water pixels to that small image, with your settings
Back to the large image and use Filters -> Repeat Last to the image.
The display is not updated until the filter is complete
This with a 4896 x 3264 photo https://i.imgur.com/yn2DaEZ.mp4
might work.