Terry, you're on the right track in asking the question here. If you want to get the water out of any line; you have to have both ends of the line open - if one end is under water, you need to blow air through it until it bubbles (though splashes would probably be a better description ) and plug it, WHILE IT'S BUBBLING. {the method has been talked about quite a bit on the forum, but if you need more info, just ask}. There are many ways that waterfalls are fed and feed into the pool, a few more specs on your system/ set-up would allow me/ us to give you 'pool specific' advice (knowing if there was a 'collection basin' or if the water just came up and poured down the trough (in which case, the water in the line would equalize to the pool water level - this may be what you were talking about in the original post ).
I hope that you are not discouraged (and pray that you are not put off on the forum) Please understand that there are sooo! many types of pools and plumbing methods, that a definative answer that covers every pool is imposible to give.