1. He passed the bakery and met one of his friends.

2. He passed a stream and became wet.

3. He passed a stream and found a bakery.
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In #2, he passed through a stream. What about in #3? Did he pass through a stream or not? Did he walk by a stream and found a bakery?

To me, all of them mean he walked by or next to a stream. If you mean that he walked through it and got wet, then you'll need the preposition "through" there, not "by."