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I own a 2006 Civic Ex with approximately 45,000 miles, all original Honda equipment (I bought it brand new)
About two or three months ago the right side front speaker quit working and I just chalked it up to be blown and was planning on replacing it.
A little afterwards, I noticed that the speaker would come in and out. I started suspecting that there was a loose wire/connection.

About a month later,the other speaker (left side) went out.

The bizarre thing is that on hot days (above 75 F) both speakers, or at least one of them works . The speakers do not work in the morning on my way to work, but if it has been a warm day , both of them will be working on my way home....I swear I'm not imagining this and I also leave the controls unchanged.

Can anyone help?

 
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Could be one of two things, on cold days I know aftermarket speakers are stiff and need some time to work in before they should be turned up loud or else you could damage them. I am not sure if that is true for stock paper speakers or not.

Second thing is it could be a lose wire behind the speaker I would not put it past with your situation. My opinion though is to take them out and start fresh.