Like January, February is a good time for visiting Japan as the weather is usually sunny and dry and sightseeing spots are not crowded. The downside of a visit in winter are the relatively short days (sunset is around 5:30pm in Tokyo) and the vegetation's barren state.
1 A healthy person drinking approximately 2 liters of water per day makes 800 to 2000 ml of urine per 24 hours (4).  If the urinary system is healthy, the bladder can hold up to 16 ounces (2 cups) of urine comfortably for 2 to 5 hours (5).
If you are wanting to know how long might it take for the kidneys to filter out some contamination that was in a glass of water you drank that is an impossible question as the contamination might be such as to become embedded in some body tissue and may never be filtered out.