Question: I'm confused with the start of the movie where he goes to the waterhole, but he doesn't drink the water. Why is that?
Question: How did Riddick know the rain would bring the monsters?
Answer: Earlier in the film when he arrived at the base, he could see the monsters from a distance when the rain came in. That's how he knew.
Answer: Earlier in the movie, they show a pack of the dog-like creatures growling at the creatures in the water. When the rain is visible, his pet starts to growl towards that direction.
Question: Who was Santana's prisoner and why did she not want to be unshackled?
Answer: Santana's prisoner was played by R&B singer Keri Hilson. Being unshackled and molested by all those men was probably the reason why.
Question: As the rain comes and the creatures come out and start to damage the station and kill people, why did the entire crew not seek refuge in their ships? Obviously, if the ships were meant for the harshness of space travel and some offensive/defensive capabilities, wouldn't they most likely have provided enough protection from the organic weapons of the creatures? It would make the plot not work but maybe should have been eliminated as a possibility.
Answer: The walls of the settlement are likely to be just as strong as the hulls of the spacecraft. It's likely they are even stronger because the settlement doesn't have to worry about weight limits. Remember also that they had to worry about Riddick hiding and getting the units back.
Answer: As he goes to drink the water, he smells it and realises it is not safe to drink.