Melissa,
I am sure you already know this, but besides keeping her in a bubble, there is no way to protect her 100% from all those bacteria out there.
Since you mentioned PA and B.Cepacia, and they both grow in the environment, it is pretty hard to know exactly what to stay away from. Obviously you can't see them. But, since they can be passed between individuals who have CF, I guess the best thing you can do is to not allow her to have any contact with those who have CF. I will say that my younger daughter has cultured PA three times, and my older daughter has never cultured it...and my older daughter is presently culturing B. Cepacia, and so far my younger one has not. But they do 'share' other bacteria, such as staph and MRSA.
There are a few things that I make my girls avoid...hot tubs (I asked the girls CF dr. about them, and he said to stay away from them b/c of the high bacteria count) and places that allow smoking (not due to bacteria, of course)! I don't let them touch the elevator buttons at the hospital or dr. offices.
I do let them swim in lakes, rivers (sometimes!) oceans and pools. They help plant flowers, but get bored with it pretty fast!
I hope that helps. I know we want to protect them, but sometimes we can only do so much. I just try to let them be little girls first.