Sometimes young children are smarter than anyone gives them credit for.
Back in 2000, a 6 year old boy shot and killed his classmate here in MI. He shot her in a hallway with a few dozen people standing around, then threw the gun in a wastebasket and hid in a bathroom. He admitted to police that he knew what he did was wrong, but the law says children at that age cannot form intent to do such things and cannot be charge with anything.
He had fights with her, he had obvious attitude problems and would spit on people, hit people, curse and make rude gestures. Students interviewed after the incident reported that they had some kind of fight on the playground, he pointed her out and told her he didn't like her.
Many people have no doubt in their minds that he intended to kill her, or at the very least harm her gravely. Children can understand what death is, they can understand what leads to dying. They may not completely understand the long term consequences of killing something or someone, but they do understand that death means you are gone and not coming back.
http://en.wikipedia.org/wiki/Shooting_of_Kayla_Rolland
I don't think this 5 year old girl wanted the toddler dead. I think she just wanted him to be quiet and the only thing she knew would make him quiet at the time was to hold him underwater. How many times have kids held their hands or a pillow over another kids face to make them be quiet? How often do they realize that their friend can't breathe or that their struggling isn't just playing?
There is negligence involved almost always, someone older should have known better. Sadly many parents don't know better and think many of the things they do is alright for their kids. Like the mother who's 13 month old drowned in the bath while she played on Facebook. She knew it was stupid but "...knew what it was like to be told no, she didnt want her baby to be told no and didnt want him to be known as a mamas boy...".