There's a (Legends) reference in Legacy of the Force IX: Invincible to a protocol droid happily walking through wind and rain. Obviously this isn't the same as waterproof, but it does imply water-resistance
Kell stared out into the darkness, noted the clustered pinpoints of
red light that floated in the pitch. He shifted on his feet as the
lights drew closer—a silver protocol droid. He attuned his vision to
Fate, saw no daen nosi. Droids were programming, nothing more. They
made no real choices and so had no lines. The false sentience of the
droid unnerved Kell and he cut off the perception.
The anthropomorphic droid strode through the wind and rain to the base
of the landing ramp and bowed its head in a hum of servos.
“Master Anzat,” the droid said in Basic. “I am Deefourfive. Please
follow me. The Master awaits you.”
and again, in The New Jedi Order: Force Heretic II: Refugee. Note that Threepio seems entirely unfazed even when the rain comes down in "great sheets".
Han and Jaina also turned to look at C-3PO now. As if in response to
the droid’s words, a peal of thunder rumbled from the tropical sky.
Fat raindrops began to splatter his metal cranium, turning what dust
was there to a reddish mud. “Threepio, are you sure about this?” Leia
Rain began to fall in great sheets across the stadium as the sides of
the troopships opened, issuing ramps. Jaina squinted to see through
the rain, trying to make out what lay inside.
And in the 1983 Marvel comic story Ellie (Star Wars #80) C-3PO is seen standing in rain.