I mostly alternate running with swimming - both are kind of hard, but since the body is used differently, I'm not using the same muscles the same way all the time. Especially gives a break to my legs. I also do 2 sessions of weights a week - (not much legs because of all the running, mostly core and upper body) for about 30 minutes, or if I take a class at the gym, 1 hour. I fit these in either with a shorter run, or a shorter swim - I mean rather than swimming 1 hour or more, I'll do weights and swim only 30 minutes, etc. It can vary week to week depending on my schedule, but I find mixing it up has helped me improve my fitness without overworking the same tired muscles.
I also throw in a session of aqua fit every so often if I'm getting overtired - nice stretching and not too strenuous - or else do some yoga for the same reason.