In what sense? As in, you don't understand the water cycle or you don't understand the origin of water on this planet?
Recent research shows the Earth's volatiles (like hydrogen and nitrogen) arrived on Earth via asteroid. Once the primordial Earth began to cool, out gassed volatiles were held in an atmosphere of sufficient pressure for the stabilization and combination of molecules such as H2O. In addition, meteorites and comets contributed to the forming oceans since they are ice-rich.
For a start there was nucleosynthesis. Elements were made from the formation and destruction of stars. Hydrogen and oxygen are number 1 and 3 in abundance of elements in the universe. Here is a link with some information about it. http://physics.info/nucleosynthesis/ - Water was present during the formation of the entire solar system. We have an extra portion here on earth because of bombardment and the gravitational, magnetic and atmospheric qualities of the earth slong with its position around the sunallow it to keep what was deposited rather than it evaporating into space.
I am going to assume that you are a creationist, and that you feel that this is a hard question for non believers to answer. What would be a creationists answer? "God did it." But how did God do it? God created the universe. How did God do it? Can you explain how He did it? The Bible doesn't give any details.
Do you believe in dinosaurs? We have fossil evidence that they exist. Was the universe created? Did it have a beginning? We also have evidence that this is correct as well. It's called the Big Bang, and yes it is based on actual evidence. Ravenevan has answered how water came into existence. The first stars to form shortly after the big bang created the heavier elements which was used in the formation of the rest of the universe. Some would say that this was all an accident, but you could also take this evidence and say, "This is how God did it." The only difference in the educated answer, is what caused it to be.