Have you ever trained for a triathlon? I find that triathlon training programs incorporate even levels of training in three different disciplines -- running, biking, and swimming. At various times in my life, I've had to cut back on running due to overuse injuries and during those times I tried to focus more on swimming, sometimes even doubling the workout (not something I would recommend for everyone). For good beginning triathlon training programs, this site has more than one to choose from: http://www.trinewbies.com/tno_trainingprograms.asp. The programs are free. So, if you're looking to cut back on running, both biking and swimming may be good swaps.
From personal experience, I know that swimming doesn't always feel as challenging of a workout as running, but to get around that I recommend a few things:
1) A music device designed for water (my favorite is the Swim iPod: http://www.bhphotovideo.com/c/product/1002620-REG/waterfi_sw3_ssi_waterproof_ipod_shuffle_swim.html). Nothing like stroking to the beat of your favorite tune to pick up your speed and take out the monotony.
2) Swim training aids ... from paddles to fins, they can take the monotony out of swimming and make your swim more challenging. I've always had good experiences buying from Swim Outlet (http://www.swimoutlet.com/resistance-training-c10805/).
3) I don't know if you check your heart rate when you run (to make sure you're working at your target rate), but if you're looking to improve your cardiovascular fitness while swimming, you should probably do the same. Keep in mind that your heart beats slower in the water and you should adjust your target heart rate accordingly. This article has more on the topic if it interests you: http://www.livestrong.com/article/166752-heart-rate-during-swimming/.
As always never stop improving and never stop having fun, but exercise at your own risk whatever form it may take.