Although a Waterpik is not as effective at removing interproximal plaque as dental floss used properly, it does seem to help cut down gingival inflammation. Most periodontists report that patients using a Waterpik device have less bleeding on probing than do other patients. Since bleeding on probing is considered one of the best measures of the presence of gingival inflammation, the Waterpik is a valuable tool for fighting periodontal disease.
It may accomplish this by causing fluid exchange in the sulcular fluids via the 'Venturi effect'. As its water pulses through interproximal spaces it may create a suction that removes crevicular fluid and any bacteria that have 'seeded' in it. This is a theory that I have heard proposed but I do not believe is a proven fact, but my experience has been that patients using the Waterpik as well brushing and flossing (or using inter proximal brushes do better when getting a periodontal exam, than those not using it.