If your E-Mail program is not set to delete mail off of the server, then it will stay on the server even after you have downloaded it. If you do not need to store it on your account, make sure your E-Mail program is deleting this mail off of the server each time you check it.

The quota on a POP box is by default 100MB. Make sure that you either delete email from your inbox, or if you use webmail, store the email in another folder to prevent interruption in your mail service by exceeding the quota of your inbox.