I have also had problems with high-impact activities due to a bad knee. I am not your doctor or physical therapist (by the way if you can get into physical therapy - these people are great), but you may have some weak legs causing problems.
There are a number of great workouts you can do. I have no clue what you have access to, but cycling (stationary bike or moving bicycle), swimming, elliptical, strength training (especially for your legs if you have knee problems), and walking are all lower impact workouts. Lately I've been doing some speed walking and it's almost like jogging. For a while I would do my own made-up circuit (modified jumping jacks, squats, pushups, situps, etc.) with the activities geared towards low-impact.
Thank you SparkPeople!
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