what type of substrate?? Sand, aquarium gravel, gravel from HD .. etc.. Either way I usually just rinse small amount of it in a bucket, place in tank, turn filter on and any cloudyness should clear up in 24hrs or so.. Generally, i've never had any prob. with new gravel clearing up.. sand is another issue..
There is a trick to doing it. You have to put only a little at a time into the bucket while you rinse until clear. If the the substrate is already in the tank, well, the only way to clear it up is with water changes. You can also stir it around making it very cloudy, then take most of the water out and re-add.