Your health care provider should have explained to you before administering your first injection that your flow WILL change. It can either start decreasing and/or cause spotting right away or potentially increase for a while as your body adjusts to the increased level of hormones. Since you didn't go back for another injection, once the first one wears off completely (another month or two more than likely) your flow SHOULD be similar to what it was before.
What really concerns me is that you're having headaches - if they provided you with the drug information (another thing your doctor should be doing) and you read it, you would have known to contact your doctor if you're having severe headaches while on Depo. If you didn't have headaches before depo, and you do now, you should get the next available appointment with your doctor to have that checked out.
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