Can taking any supplement for a period of time lower the natural levels of the supplement after it is all done? creatine, glucosamine, vitamins, etc?

Yes it can: Creatine, along with phosphate, occurs in the body naturally as a very important component of your energy metabolism system. Research has shown that the effects of supplements of combined creatine phosphate are due to increased muscle mass, making this supplement especially useful for athletes who are involved in "short burst" activities, such as lifting heavy weights, making tackles as a football.