Is Spacek wearing coloured contact lenses?

I'm guessing they had her wear brown contacts because Anne Bancroft also has dark eyes. The actresses don't resemble each other at all, which I found a little distracting. Sissy's bright blue eyes would have really made the mother/daughter pairing hard to believe.

Yes, she was wearing brown contacts.

I think they did this because it was easier to see her as being plain and dowdy.

Those bright blue eyes that she has in real life would have made her too attractive for the movie.