Taklin Chadtin (one of the commentaries on Yerushalmi) says that the rule is that if a person is meticulous in observing a certain mitzvah this will protect his children. However if he isn't always so careful, even though he is known for his zealousness on this issue, he could be punished for it and this was the case with Nechunia who was not always so careful in his dealings with the public regarding water. However after Rabbi Pinchas ben Yair was certain that the father of the girl was always meticulous about the matter of water, he prayed for his daughter and she was saved.

Other commentaries explain that the difference between the cases is that in the second case Rabbi Pinchas Ben Yair was on hand to pray and demand justice for the girl and this is the meaning of the angel in the form of Rabbi Pinchas. A Tzaddik's prayer can save lives and therefore people go to Tzadikim when they have life issues, as "A Tzadik decrees and Hash-m fulfills" (Taanis 23a)

I thought of another possible explanation. In the first case the son may have died of thirst because he was not following in the footsteps of his father. If a father is very meticulous but his son does not maintain these standards, he is held accountable. However in the second case the daughter was about to get married and was a devout person and therefore her father's merit protected her when she fell into the water.

Yoel Domb