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We have a small stream that cuts through our yard. The dog enjoys drinking from it frequently, even when he has a source of fresh water (from the kitchen sink) nearby.
Is it safe? If not, is there a way to discourage him from drinking from the stream and encourage him to drink from his bowl?
Generally speaking, if you are not familiar with the water source, it is not safe to let your dog drink from it.
Leptospira, which is a genus of bacteria excreted in the urine of infected animals, can survive for many months in water ways, so our vet has recommended that in addition to his normal annual shots, he also be inoculated for leptospirosis.
Beyond the additional inoculations, our vet has not shown any serious concerns though. However, it is always advisable to consult with your vet as there may be pathogens that are common to waterways where you live.
Frankly speaking in my experience, you can't really discourage your dog to not drink from the stream you mentioned. I see and I don't know exactly why but dogs like drinking from foul places. We tried to resist our dog and even tried to reward him if he drinks from the vet meant for him but really, this is one case where we could not really discourage him. However if you talk about health, we haven't found a clue which tells us that he felt ill for that. So if the source of water is clean, there is nothing to panic about. However, which owner does not want his dog to be distant from foul places? In that case, I would suggest taking physical measures (such as boundary or fence in your garden) to resist him from going there.
