What was the movie that had an animated scary owl singing while a house flooded?

You're likely thinking of the movie "The Nightmare Before Christmas" (1993).

In the scene you're describing, the character Oogie Boogie, a giant, stitched-together sack of bugs, sings a menacing song about flooding the town of Halloween Town. The animation style used for Oogie Boogie is a mix of puppetry and stop-motion, making him appear to be a scary, grotesque owl.

Let me know if this is the movie you were thinking of!