Both milk kefir and water kefir are the fermented products and the results of good bacteria digestion of carbs. As the name suggests water kefir and milk kefir bacteria use different habitat.
Similarly to milk kefir during fermentation bacterias digest naturally occurring lactose, in water kefir sugar needs to be added to the fuel fermentation process.
As final product milk kefir is more like food with all proteins, calories, and a rich variety of microelements while water kefir is a type of e beverage yet with positive strains.
Milk kefir has more probiotic strains and fewer carbs compare to water kefir which with fewer strains and more sugars.