Go through the wall of water and head inside the cave behind it. Inside you will come across a deadly Spriggan Earth Mother, who has lots of health points and a very powerful attack. In fact you don't need to fight her - just soak the taproot in the water (you do it by "using" the river).

How do you activate Headwaters?

At the top of the dry bank on the right is a lootable skeleton in front of an unlocked boss level chest. If you are here as part of the relevant quest, you may activate the headwaters by looking at and "activating" the shallow pool. There is nothing else of interest in the cave.

How do you get taproot in Skyrim?

As mentioned, taproot can be either bought from an alchemist or obtained from the corpses of spriggans. The unmarked Giant Nirnroot Island is a convenient location to obtain taproot as it is home to three leveled spriggans. Once they have been obtained, proceed to the Headwaters of Harstrad.