1. You swallow the water, and it goes down the esophagus, into the stomach, duodenum, through the small intestine and then to the large intestine.
2. The large intestine (or colon) is where much of the water is absorbed, and absorbed through the wall of the intestine, through an "osmotic gradient". For complete details see item 2.3 here:http://www.gastroresource.com/gitextbook/En/Chapter11/11-2.htm
3. This water is then absorbed into the intracellular space, and then flows into the blood vessels in the area.
4. The fluid in the blood vessels travels around the body, first to the liver, then to the heart, then to the lungs, then back to the heart, then through the aorta down to the kidneys.
5. The fluid in the blood is "filtered" through the kidneys.http://en.wikipedia.org/wiki/Renal_physiology
6. The water, now urine, collects in the kidney and is sent through the ureter to the bladder, where it sits until the body releases it through the urethra, and hopefully into the toilet.