Known issue with Apple Mail and El Capitan.

Problem:
After upgrading to El Capitan, Mac mail prompts for the email account's password but won't accept it.

Resolution:
Restarting the computer and disabling mail accounts in the process, then adding them back on account at a time resolves the problem.

Here is how to Temporarily stop using an account in Mail

Choose Mail > Accounts, select the account, then deselect the Mail checkbox; the account’s messages are no longer shown in Mail.

To use the account again with Mail, select the Mail checkbox; the account’s messages are shown again (they don’t need to be downloaded from the server again).