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In theory a dog drinking untreated water could contract disease. Common diseases include E. coli, Salmonella, and giardiasis. The first two are bacterial diseases that can cause illness and are caused by fecal contamination of the water supply (i.e. wildlife defecating in/near the stream). Giardia is an intestinal parasite that can cause mild to severe diarrhea and sometimes nausea. Although uncertain, this parasite may be transmissable to people. A vaccine has recently been developed to help reduce the symptoms and the chance your dog can transmit the parasite to you. It has not, however, been shown to prevent the disease considerably in the dog.
Having said all that, most dogs in most situations are going to be just fine. Consult with your local veterinarian for more questions.
Hope this helps.
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