I'm using a Water Reflection asset from the store which requires URP. Once I switch to URP 2D Template, the water works, the game and everything works, but Naninovel assets do not show at all.

It's clickable, but not visible. Naninovel shows fine in the hierarchy and everything, it just doesn't show in the game (inputs,backgrounds,textprinters,choicehandlers, etc.) but if I blindly click them where they should be, or type in an input where an input is due, it registers fine. Looks like only a visual issue.

Anyone know the issue?

The documentation says there's nothing needed to be done when switching to URP if I understood correctly

It's probably a render priority/queue issue with the water reflection shader. I suggest temporarily disabling it to confirm whether it's the cause.