How can I get mail to stop putting email in the junk folder?

If you've shut off all junk mail filtering on all devices accessing that mailbox, then your ISP is doing that filtering.

What color are the junk emails? Do you have the ability to mark as non junk?

If you are using IMAP, then it may be your provider that is marking the messages as Junk. Is this happening with both accounts, or just iCloud or gMail?

If the junk filter in Mail were marking them as junk, then they would be brown and would have the tab to mark as Not Junk. The default coloring of the text and no tab for Not Junk means they are being put in the Junk folder by your provider. I assume your Junk mailbox for that account is mapped to the Junk mailbox in Mail. They are junked on the server and being synced as IMAP to the Junk folder on the computer.

Which account do those messages belong to? I will assume they are probably Gmail. Is that correct? If you go to the webmail site, you will probably be able to mark them as non-junk there. Check filters there that might be putting them into the Junk folder.

kguess wrote:

They look like other emails and I cannot mark them as junk or non-junk. Before I turned off junk mail, they were not marked as junk either. I could mark them as junk, but since they weren't marked, I couldn't do anything to tell Mail they weren't junk except move them into the inbox.

If you are certain that all of your computers and devices accessing this mailbox are not running local junk mail filtering, then log into and check the web interface for your particular mail provider — most mail providers offer a web interface — for any and all junk mail settings that might be available from your mail provider in the web interface, and then check with the support folks for your mail provider.

There are no settings on iOS devices for Junk filtering. You can only view a Junk mailbox synced through IMAP. Only on the Mac can you create junk filtering.

You've already said they are not brown and no tabs exist to mark as Not Junk. That means your mail provider is doing this. Gmail does have spam filtering, but no settings for it at the webmail site unless it's done in a filter there. You will need to verify at the site if you can mark them as Not Junk.

For iCloud, there are no settings either at the site. But they still can be sent to Junk by the server. But junk filtering does sync with the iCloud.com website and usually can be marked or unmarked either at the computer or website.

So that's why I believe that your problem is with Gmail, but you never indicated which account that the problem lies with.

It really has nothing to do with your ISP or their mail since it's not their mail getting sent to Junk. I guessed Gmail, but you say it's iCloud addresses being junked.

Go to iCloud.com and check and see if you have the ability to mark them as not junk there. If not, then they are being junked by the iCloud server and you will have to call them. Only they can reset that.

When the junk filter puts messages in the junk mailbox, they should be colored with brown text. If they aren't brown, then it's not the junk filter putting the messages to junk. So, what color are the messages you can mark as Not Junk?

The fact that you can mark those as Not Junk means Mail probably put those there, or a rule at iCloud.com flagged them as Junk.

For the messages you can't mark as junk in the junk mailbox, they were not put there by Mail. They were either put there by the server itself, or some rule is moving messages there or corruption is moving messages to that mailbox.

You can try rebuilding the mailbox, or reindexing mail in case messages are not being tagged correctly.

Mail (El Capitan): Rebuild mailboxes

Note: Instructions below show V2 folder. It's actually the located in the V3 folder.

http://osxdaily.com/2013/08/01/rebuild-mailbox-reindex-messages-mail-mac-os-x/

One way to test this is to sign out of iCloud, or disable iCloud email on the computer and use the website for testing. If messages that normally go to junk start going to the inbox, then you can say it's something corrupt on the computer. If they continue to go to junk, then you will have to call Apple and have them deal with it. While at the iCloud.com website, make sure no filters are set to flag messages as junk.