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I just dead headed all my salvias about a week ago and they aren't looking so good. Also, it's been raining like crazy the past week.. maybe this has something to do with it? The leaves are turning brown and whole stems are dying. Any ideas as to what's going on with them?

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As a start, it is highly unlikely that the plants will die from this.

This is something that I've seen very frequently with members of the mint family and shouldn't be a huge concern. Growing up, our various mints would get something like this on occasion and they still grew like weeds year in and year out.

On the one hand, I don't think the exact cause of the brown leaves is known, but it is usually associated with a highly stressed plant that is trying to protect itself. Some of the leaves look like they might have been attacked by a pest and others look like it's just the plant reacting to a potential infection vector. If you recently got a surprising wet surge in your weather, it might have given various bacteria a boost in strength, or with the dead heading it might have decided to put energy into new shoots. However, one thing that I'd be a little bit careful of is root rot, as you mentioned the rain. If your soil isn't draining properly it can also cause symptoms akin to this.

If you want a bit more reading about salvias in general, this has some excellent information.

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