Creepy old house that looks like it is in another country. Movie starts with two children running away from an old lady that looks like a witch. The lady that looks like a witch was wearing black and peeking aound a lage tree. The little boy falls into the creek and appears to drown but he turns into a cartoon. He meets a seal or some underwater animal and become friends. I remember seeing this on TV in the early 80's.

Second part of your description sounds like it's from The Water Babies (http://www.imdb.com/title/tt0078477/)

Movie about a priest who gets sent into new countries to preach christianity to indian tribes back in the 1400 to 1600 centry