Joints do snap, crackle, and pop at times and this is normal. However, if your knees click or pop EVERY time you do a motion such as going up/down stairs, standing/sitting, or squatting that is something that you need to address before it becomes a problem.
The clicking that you hear is your knee caps pushing against your knee while in motion. This happens due to muscle imbalances in your body, either your hip is weak and your knees are caving in with bending or the arches in your ankles are weak and your knee is again caving in and causing this sound. If you don’t start addressing these muscle imbalances soon the bones wear down and arthritis could begin to form.
Here’s a quick test for you, stand in front of a mirror or have someone watch you, and perform a squat. Watch (or have your friend watch) to see if your knees are staying in line with your feet, or if your knees are moving in between your feet, also listen for any clicking sounds. If either of these are the case you may have ankle instability or hip weakness. You should see your Physical Therapist for an evaluation to make sure that this problem does not get worse.