How can I use water fitness in the rehabilitation of a running injury?

Water Rehabilitation. Water rehabilitation is a good form of therapy because it is generally non-weightbearing. The water provides good resistance without putting additional stress on the injured body part.
Great therapy but... Water fitness is a great form of therapy for running injuries, but it also depends upon the type of injury. You probably should be seeing a physical therapist to help and recommend proper exercises, etc. A range-of-motion massage therapist is also an excellent option.
Targeted P.T. Depending on the injury and anticipated recovery time, specific hydrotherapy recommendations from a licensed physical therapist can be invaluable. In conjunction with other types of treatment (rest, passive/active exercise, analgesics, bracing) whirlpool baths can help quite a bit.