In more natural way you may say

你跑得好快！

or

你跑得真快！

“跑步” here is a noun means the task/work you done of running.
When you use “跑得” after “跑步”, you are pointing to his state of the running.
But just “跑步” is also OK to meaning the state.

“跑” means the act/action of run,
When you use “跑步” instead of “跑”, you are specially pointing to the hole task/cycle of the running, it’s very fast. If just pointing to a short action/state, just use “跑”

Also, like in English we natural say

You runs quite fast!

in Chinese it’s natural to say

你跑得真快！

“跑步” here is a noun means the task/cycle you done of running.
When you use “跑得” after “跑步”, you may want to pointing to the state of his running act/action,
It’s causing conflicts.

“跑” means the act/action or general state of running,
When you use “跑步” instead of “跑”, you are specially pointing to a task/cycle of his running. 
If just pointing to a short action or general state, just use “跑”

你跑得很快！

If you are pointing his running cycles, use

你跑步很快