OptiFine:
Animations directory: assets\minecraft\optifine\anim\
Delete the properties file for the corresponding feature that you wish to remove

McPatcher:
Animations directory: assets\minecraft\mcpatcher\anim\
Delete the properties file for the corresponding feature that you wish to remove

FabricSkyboxes:
Sky directory: assets\fabricskyboxes\sky\
Delete the json file for the corresponding feature that you wish to remove.

Nuit:
Sky directory: assets\nuit\sky\
Delete the json file for the corresponding feature that you wish to remove.

Celestial:
Overworld sky: assets\celestial\sky\overworld\sky.json
Open the json file, and delete the full quoted line along with the comma from "sky_objects", that you wish to remove.
(Make sure each sky object remains separated by a comma, otherwise the file will break. The last line must not have a comma after it!)
______________________________________________

Bubble column:	sky2 / bubbles_1 + bubbles_2
Fish swarm:	sky3 / fish
Shark: 		sky4 / shark
Whale:		sky5 / whale
Leviathan:	sky6 / leviathan_1 + leviathan_2