Something Chris Brennan (old school MMAist) recommended was to get in the shallow end of the pool, and shadow box. He felt the added resistance of the water helped with conditioning, without sacrificing form by overlaoding the movements.
Other ideas for conditioning:
As long as you are a decent swimmer, there are a lot of things you can do to increase the effect.
Try swimming with a full sweat suit on. Another thing I have done before (it really sucks), is to wear a sweat suit, and swim holding the center of a towel in each hand.
Try hypoxic swimming, but ONLY if you have a friend or someone there to watch you. Hypoxic swimming: swim using whatever stroke you want, but you pick a number, and only breathe every so many strokes, ie, for a two, you would breathe every other stroke. Once you get used to the idea of it, try pyramids. Start at breathing normal, then go to 2, then 3, etc, stopping short of blacking out. LET ME REPEAT: YOU WILL FEEL SHORT OF BREATH (CONSIDERABLY), BUT IF YOU START TO FEEL LIGHT-HEADED OR SOMETHING LIKE THAT, STOP. When swimming, always err on the side of caution, and like I said, if you try this out, take a partner with you for safety. Shallow water blackout is a killer.
That said, you will learn you can work harder than yourealize when you feel out of breath.