Oh my God... you have a hamstring strange and you are Pool running!!! That is literally the worst thing you can do as well as biking.
Don't worry because I didn't know this either :) I had a hamstring strain and because I didn't realise it was the pool running, biking and elliptical that was preventing my injury from healing and making it worse, I ended up tearing my tendon (grade 2) at the attachment to the bone. It has taken me 7 months so far and I am still in a minor discomfort. But I can run very easy. Before this I was running 65 miles a week average.
So how I treated mine from unbearable pain to what now is a little uncomfortable is NOTHING that creates a dragging sensation OR the motion of running. For example you are using you hammy to pull a pedal, pull you through the water or pull the elliptical/ x-trainer round. Stop that because it will only aggravate it further.
ICE has been the only thing that has saved me! A bag of crushed ice works wonders. DRY NEEDLING is something I have found very useful as well as sports massage, foam rolling, and cross friction massage/ trigger point with the foam roller.
3 weeks really is not a long time to have out for a hammy, you would have lost barely any fitness at all trust me. For cross training I found that pull buoy swimming helped me massively as to not use your legs but still get your HR up. After all my time off I returned to running shortly and of course, I felt a little less fit but not half as much as I was expecting :)
Don't panic- there are ways around it if you really want it. I thought mine would never go and I proved everyone wrong! Good luck
G