If you clean your substrate just clean it in some of your tank water, not plain water. Works best to fill a bucket with one third sand, up to two thirds water then use hands to swirls sand. You just want to put gunk into suspension so you can pour it off sand into second bucket. Pour first bucket sand into new tank and reuse water in other bucket, to rinse more gravel/sand. All your removing is any gross amounts of filth. If your water becomes really filthy before your finished with all your gravel, use some new "old" tank water. Never use fresh (unmixed) water to rinse sand as it will kill off all beneficial life including bacteria. The deeper your sand bed is the more likely you will have some cycle problems. With shallow gravel/sand usually all you have is detritus and some planktonic life, not a lot of beneficial bacterias, as the oxygen levels are too high.
