This is Doms explanation of the difference between water kefir and milk kefir
http://users.chariot.net.au/~dna/kefir-faq.html#probioticeffects
WHAT ARE THE PROBIOTIC OR OTHER BENEFITS BETWEEN A TRADITIONAL MILK-KEFIR AND WATER-KEFIR
This is a good question, which is currently difficult to provide a direct answer to. Regarding beneficial effect of kefir, and yogurt e.g., seem to give benefits in which are said to be different mechanisms involved, and which most importantly are restricted to certain individuals rather than to the population as a whole. This is current understanding of the benefits of probiotics in general.
In my personal experience, I have recovered fully from Hepatitis C infection [genotype one] including Ulcerative colitis, which I put down to regular intake of milk kefir and milk kefir-grains, with the inclusion of frequent rectal injections and retention of milk kefir-grains.
I'm not aware of any current scientific research regarding the benefits of water-kefir, let alone differences between benefits of milk-kefir Vs water-kefir. However milk kefir exhibits anti-bacterial [inhibiting the growth of unwanted bacteria], anti-mycotic [inhibiting the growth of unwanted molds or fungi], anti-neoplastic [inhibiting or preventing the growth or development of malignant cells] and immunomodulatory [an immunological adjuster, regulator or potentiator] effects, including a recent study of the anti-inflammatory activity of milk kefir, especially so for kefiran, which milk kefir-grains consist of and exude into the kefir during fermentation of milk. Apart from the anti-inflammatory effect, the former four activities may be shared by water kefir-cultures. Milk kefir also contains a powerful antioxidant, [1] existing as charged molecules. [2] The former research has shown it to be more powerful than vitamin E in protecting body cells against oxidative damage. The latter research concluded that the pH and heat resistant powerful antioxidant of milk kefir, whether made from dairy milk, rice milk or soymilk, has the potential to prevent pathogenesis of the brain such as Alzheimer’s disease, Parkinson’s disease, ischemia from stroke, Huntington’s disease, dementia with Lewy bodies and amyotrohic lateral sclerosis. There has yet been similar studies to evaluate antioxidants of water kefir that I am aware of at this point. Milk kefir also has the ability to correct high blood pressure and blood glucose levels.
Depending on culture-process, may determine the outcome regarding possible benefits of the final kefirs used for consumption. A milk-kefir consumed at a sweeter stage will produce different probiotic or other effects for certain individuals, over ingesting a sourer, or ripened kefir. Some have found that a sweeter milk or water kefir has a laxative effect, while sourer kefirs may produce a constipating effect for the same individual. This seems to be for both varieties of kefir. On peristalsis action alone, I've found that a sourer milk-kefir taken in the morning, will produce a stronger peristalsis action over ingesting a sweeter kefir [in myself personally]. A water-kefir does not seem to induce a similar action. Although I've found that this may vary with individuals, for a neighbour recently tried water kefir for the first time, and had to evacuate his bowels shortly after drinking the beverage. I could hear his bowels gurgling within seconds of having the water kefir! HOwever, his diet is rather poor mostly consisting of heavily processed foods, so one has to consider the condition of the GI tract and general health, and the normalizing effect either type of kefir has on the human organism as a whole, especially in regards to gastric function.
So far I've mostly found this to happen with certain individuals who have tried a milk-kefir for their first time, but this case has proven that water kefir can also do the same.
Taking a sweeter milk or water kefir may increase the counts of certain organisms of the Gastro-intestinal [GI] tract. A sourer kefir may provide other benefits e.g., increasing liver and gallbladder function at the cost of a less counts of specific organisms in the GI tract. A sourer milk or water kefir may have a mild diuretic effect. This effect is shared by water-kefir cultured for 48 hours [usually more pronounced if taken on its own]. Although a water-kefir has a tendency to induce the passing of urine within 30 minutes after drinking and in some cases the frequency may be every 10 to 30 minutes for a few hours. This can be seen as moderate modulating diuretic effect, which may be beneficial for specific conditions such as oedema. I personally feel the diuretic effect is quite pronounced in the stomach and non specified areas in GI tract, where there is existing inflammation. As the inflammation is reduced, then there is less of a diuretic effect with the intake of kefir.
On nutritional value alone, milk-kefir has a superior nutritional value over water-kefir. If milk-kefir is ripened at room temperature [or in the fridge] for 2 days, Folic acid content will increase by over 110% in comparison to freshly strained kefir or fresh milk.
I've personally observed the benefits regarding certain individuals who have ingested milk-kefir to successfully heal Peptic and gastric ulcers, both on onset and advanced stages of the disease. I'm not certain whether water kefir-grains will give a similar result?
A water-kefir made with the addition of medicinal herbs [Kefir d'erba medica] should include the benefits and or side effects of the individual herb used in the preparation of the probiotic herbal beverage. The final culture-product may include the propagation of certain microbes, which are native to that of the microflora found on the actual fresh or dry herb used in the culture-process e.g., Lb. plantarum. Where as not all milk-kefirs may contain this particular strain or other strains of friendly bacteria native to the microflora of vegetables and herbs. However, I have found that a herbal water and milk kefir, prepared with certain herbs such as Chinese Angelica root, including Korean Ginseng, induces a a unique feeling of euphoria shortly after consuming the beverage. This may tell us that the fermentation process increases the bio-availability of specific compounds of certain herbs with therapeutic properties. Or, psychoactive compounds with a short half life may be produced through fermentation.
Kefir has a vast microflora, of which the evolution is dependent on the duration of the culture process. A sweeter kefir [kefir fermented for less time] will contain a unique microflora over a sourer kefir [longer fermentation]. On the other hand a more acidic kefir, or a well ripened kefir, acid-loving lactic acid bacteria such as Lb. acidophilus and Lb. Brevis are found in higher proportions at the end of fermentation. Where as Leuconostoc mestenteroides and others, initiate the fermentation, then fall in numbers as the kefir becomes more acidic. This is due to Leuc. mestenteroides are unable to tolerant the amounts of lactic acid that they and other organisms produce as a metabolite of lactose. So, along with other similar microbes, they eventually commit environmental suicide ... poor little micro-chaps. Where as Lb. acidophilus and Lb. Brevis are acid lovers and can better tolerate acidic conditions. In effect, if one has any knowledge regarding microbiology of kefir at a specific level, one may tailor-prepare a kefir to achieve a specific goal.
Interferon-beta induction of milk-kefir. Milk-kefir was found to enhance interferon-beta secretion in body cells. Interferon is a glycoprotein produced by cells in response to viral attack, such as Hepatitis, whose function seems to be the triggering of viral interference defence mechanisms in uninfected cells of the same species in which it was produced. Interferon is believed to be effective against viral diseases, possibly including some forms of cancer. It was found that kefir enhanced interferon-beta secretion of a human osteosarcoma line MG-63, treated with a chemical inducer, poly I: poly C. The active substance in kefir was found to be sphingomyelin [SpM]. SpM from kefir was a mixture of four molecular species of SpMs having C21-, C22-, C23- and C24-fatty acids. It was found that kefir fermented milk SpM enhanced interferon secretion 14 times, while SpMs from other sources such as yogurt enhances only 2 - 3 times.[3] These findings were found in vivo and in vitro.
This is possibly why kefir is unique in that it gives the consumer a distinctive increase in sense of well-being shortly after ingestion, where yogurt, buttermilk and other culture milk-products do not induce the same effect, or it is not as pronounced. Kefiran, the unique polysaccharide of milk kefir-grain organisms, has a calming effect.
NOTE Sphingomyelin can accumulate in a rare hereditary disease called Niemann-Pick Disease, types A and B. It is a genetically-inherited disease caused by a deficiency in the enzyme Sphingomyelinase, which causes the accumulation of Sphingomyelin in spleen, liver, lungs, bone marrow, and the brain, causing irreversible neurological damage. Of the two types involving Sphingomyelinase, type A occurs in infants. Children with this type rarely live beyond 18 months. It may be important for individuals with Niemann-Pick Disease consider omitting sphingomyelin containing foods such as Kefir, Yogurt and Buttermilk etc. Although I have no actual evidence at this point, that externally derived Sphingomyelin is associated with this disease or is a cause for problems in such cases. It's simply information that I've recently come across and thought it should be mentioned here as a precaution, and for further investigation.