Note 1:
The instructions herein are made obsolete by the addition of support for Respackopts.
Download from https://modrinth.com/mod/respackopts and use the gizmo in the resource pack selection screen.
(you can still you the manual method described below, if you really want to)

Note 2:
If you're using Celestial 2.0 to use the pack, you may still use the manual method below, as with Respackopts,
the in-game chat will spew out errors from Celestial if you disable any features. This does not break the
pack in any way, it will still work perfectly fine, but in case that bothers you, do it manually.
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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!)
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Bubble column:	sky2 / bubbles_1 + bubbles_2
Fish swarm:	sky3 / fish
Shark: 		sky4 / shark
Whale:		sky5 / whale
Leviathan:	sky6 / leviathan_1 + leviathan_2
Magnapinna:	sky7 / magnapinna_1 + magnapinna_2