Do i need to be concerned with the long term affect on my knees due to daily running?

Running & knees.: Running is hard on the knees. We accept this because the health benefits of aerobic exercise are myriad. With proper running technique and proper footwear, one can minimize the impact of running on the joints.

In general no: there's a long-term study of runners at Stanford and in general the knees do fine. I would add though that we need to make sure that there can be no mechanical issues with your knees, and the type of knee you have