YES, doing Atkins and increasing exercise can definitely cause your hormones to be so out-of-wack that your periods will be affected, no matter what kind of birth control you are on (or even if you AREN'T on any). I am on the pill, not Depo, and I have been having regular, light periods for 7 years (while exercising)...never any spotting. But when I started Atkins, I had a whole period in between my regular periods, not just spotting...we're talking lots heavier than my normal. Your body should even-out and return to normal after 2 months on the diet...that's how long it may take to get adjusted. Doctors always want you to come in and get checked so they don't give misleading information and cause you to do further damage, but I find that just "stopping in for a checkup" is never that easy...it's a huge process just to make an appointment, take off work, and wait and wait and wait and then finally get to see the doctor for 5 minutes...I'd say give it about two or two and a half months and see if you are still spoting, then see your doctor for further testing if you aren't back to normal.