I remember watching a movie as a child that had live action with actors about a farm and a flood, as well as animation with chickens and some other animals this was a children's movie either in the early 90's or late 80s.

I'm aa big movie buff and I know what movie your talking about but for the life of me I cannot remember the name... here's a website with a list of around 100 children's movies from various years going all the way back top 1933 in some cases.. maybe your movie is in there hope I helped http://www.filmsite.org/100kidsfilms.html

Was it rock-a-doodle? That involves a farm and a flood and a rooster who sings like elvis!

Yea that is rock a doodle!! I love that movie!