Jean's Phoenix powers were increasing throughout the movie. I guess at the end she was powerful enough to hold the water back. You noticed she started bursting into flames...

As for Magneto, he shut Cerebro down before he entered. Remember the part where Xavier said "That's strange" and started messing with the controls. Plus Jason/Little girl was surprised and worried because something had gone wrong (and all the mutants stopped writhing in pain because Cerebro was shut down)