I collected substrate from a local river years ago, and am still using it. It was a long process to clean, but worth it IMO. I scooped it up from the river bed in a aquarium net and rinsed it in the net while in the river to get rid of most of the fines. I then rinse a couple pounds at a time in a plastic tub with tap water (outside) to get rid of any other fines or organic matter. Then bleached the sand to kill anything left, rinsed again, dried, and then used a 2mm sieve to get the larger grains out.
I kept rays on this substrate for several years w/o any problems. I did use coated sands prior and had issues.