When the user joins up, you add a field to his membership which is "waiting", and a GUID value to match. You then send an email containing a link to a "Complete Registration" page which has the UserID and the GUID value as query string parameters:
www.MyDomain.com/Login/ConfirmEmail.aspx?uid=1234567&emid=ba1b3a6f-5b47-41e0-b09b-d503dbdfe858
In the page, you check the uid, the status, and that the GUID matches. If so, you change the status to "full member" and let him proceed.