Its interesting how this topic rolls around. In the saltwater aquarium world they used to sterilize everything... then they discovered live rock... and now every decent reef tank has live rock... some is even cultured in the wild.
Similarly, freshwater aquariums used to use only a thin layer of substrate for fear of anaerobic regions, now we use deep soil substrates (or at least I do). Others are trying to get rid of snails... I think they are key to my low maintenance approach.
So back to your question. I have used substrate directly form the stream without any treatment at all... in fact, contrary to Nick, I made sure to keep it wet to keep it alive. You will occasionally get a critter... hopefully nothing that flies around the house too much. But nothing that will hurt the aquarium (unless you have small fish and get a dragonfly nymph). I did have some problem like the old live rock tanks did of having an algae bloom from too much live stuff all getting put into the tank at once and some of it dying off... I would suggest either doing this early when you are cycling the tank and can tolerate it being less than pristine... or adding it slowly over a week or so to allow things to acclimate and even out.