The story of Jesus walking on the water appears in three of the canonical gospels — not, as you might think, the three Synoptic gospels (Matthew, Mark, Luke) but, rather, the gospels of Matthew, Mark and John. I have no idea why Luke’s gospel leaves this story out, but it’s not too hard to see why life-of-Jesus movies have skipped this episode for the most part.*
For one thing, it’s more brazenly supernatural than some of the other miracles, which could be a turn-off to some of the more skeptical or liberally-minded audience members. Also, it’s kind of hard to visualize what it would have looked like, exactly, for someone to walk on water — especially when there was a storm raging all around him and stirring up the waves. Until the rise of CGI, it might have been too difficult to film a version of this scene that would have looked half-way plausible.