Never encountered the problem. If you are dealing with snow melt, usually there is plenty of water close by. Seeps I have encountered in the desert sometimes were improved by digging, but even this was fairly rare.

On my favorite route on my favorite mountain in Arizona, we would pass by Juniper Seep, frequently dry as a bone, but often offering water that could be scooped with a cup - delicious!!

I would just use the tube to suck the water out or start a siphon if possible.