This issue appears present in nearly all 1.16 snapshots and pre-releases.
During rains, rain will occasionally permeate through blocks no matter how many blocks are above it. This is especially apparent in caves.
Comments 3
The "Clouds" and "Graphics" settings appear to have no bearing on the issue. The world was started with "Clouds" and "Graphics" set to "Fancy" and any changes to those 2 settings did not impact the bug.
See MC-179845
Do you have "Clouds" set to "OFF" and "Graphics" to "Fancy"? If so, duplicate of MC-163575.