If your rabbit is having true watery diarrhea and it isn't stopping, that is an emergency and you should get her to the vet right away, as rabbits can dehydrate very quickly. If it is just soft mushy poop, it can have various causes. Parasites/bacteria can sometimes be the cause, but most often it has something to do with a rabbits diet. Either a food introduced too quickly, an intolerance for a certain food, or too many carbs and sugars in the rabbits diet. If you are experiencing soft poop with your rabbits and it happened after giving a new food, stop giving that food and see if it clears up. If not you may need to feed grass hay only for a few days until the soft poop clears up, then slowly reintroduce pellets and veggies, one thing at a time, starting off with small amounts.
Sometimes some rabbits just have a low tolerance for certain foods and just can't have them, or not very much, or it starts causing problems. I have one rabbit that can't have pellets at all or he'll get sick, another that can only have a small amount of pellets or she'll get soft poop, and some of my rabbits can't have treats and can only have very specific veggies. If you have to stop veggies and pellets for a short amount of time, then reintroduce them, doing it one at a time helps you to pinpoint the possible problem food. It could be one or more veggies, or it could be from getting too many treats and/or pellets in the diet causing a gut flora imbalance. It's called cecal dysbiosis. If you want to check these links, they explain it pretty well.
http://www.sawneeanimalclinic.com/downloads/chronic_intermittent_diarrhea_in_rabbits.pdf
http://www.veterinarypartner.com/Content.plx?P=A&A=3012
If the soft poop doesn't clear up, your rabbits condition deteriorates, or you suspect parasites, it would be a good idea to get a fecal test done by your vet, just to rule it out.
eace
