While paddling his canoe at the place on the river where the water turns black (this is a real phenomenon caused by decaying vegetation that stains the water.) Father Mahoney sees a river dolphin. (The Amazon river dolphin is found throughout much of the Amazon river basin. I saw a few of them when boating in the upper Amazon.) Then Mahoney sees a naked woman emerge from the water and walk onto shore and into a hut. He follows her there and she removes the cross from around his neck then puts it around her neck. They they kiss.

The rest of the movie deals with the boy, called the dolphin boy because he rides the dolphins that protect him from dangers such as caiman (a type of alligator.) But the dolphins can't protect him from the greedy and violent men who discovered gold in the area and kill his mother then kidnap him and bring him to the city. O'Reilly finds the boy and knows that the cross around his neck proves he is the child of Mahoney. He calls him Lazaro because he has risen from the dead and sends him to an orphanage.

The snake scene is very short and unexpected enough to be shocking. The snake we see is not real, it's only a simple prop, but the effect is real enough. We only see the snake in brief close-ups, but that's better in my opinion than seeing too much of a fake snake, or worse, a bad CGI snake. The snake is probably supposed to be an Anaconda, the largest snake in the area. The snake's action is unrealistic, but in the movie's world of magical realism where a dolphin turns into a woman, I think it's more symbolic than real. It is only meant to represent what happens to a priest who broke his vow of chastity and lost his faith. The cross he loses obviously symbolizes the protection of his faith, and it continues to represent protection in the rest of the movie for Lazaro and then for a friend he gives it to.