As long as you do not experience an actual flow of blood (see here for a discussion of distinguishing between a stain and a flow), you may take precautions against becoming niddah from this staining. This is true even if the staining occurs consistently every month.

Blood found on toilet paper may be disregarded and does not render you niddah as long as you waited at least a few seconds after urinating before wiping. Blood found in the toilet bowl or on the toilet seat can usually be disregarded, but if it is found within seconds of urinating a question should be asked.

There is no requirement to look in the toilet or at the toilet paper. If you want to check toilet paper to be aware of any staining, we recommend that you wait at least a few seconds (ideally 15 seconds) before wiping and then look at the toilet paper, since blood found on the toilet paper in such circumstances would not make you niddah.

The five day minimum begins when you actually become niddah. Since you did not consider yourself actually niddah until day 3, that is the point you may start your five day minimum, even though you separated earlier as a precaution.

Going forward, unless you experience a flow, you should wear colored underwear or disposable pantyliners, and wait 15 seconds after urinating before wiping to avoid becoming niddah from the staining. We do recommend abstaining from intercourse until 24 hours after the staining subsides even if the staining does not make you niddah.

Please feel free to get back to us with any further questions.

B’Hatzlacha!

This response has been updated to reflect the rulings of our current Rabbinic Supervisor, Rav Kenneth Auman, regarding waiting before wiping.