Todays daf (Shabbos 14a) has a whole slew of gezeras relating to טומאה and טהרה. Among them is a gezera that anyone who takes a shower becomes a שני לטומאה and is מטמא תרומה. The reason being that the chachamim were afraid that people would think a shower is as good as the mikva. Although this gezera has no relevance nowadays, when the Beis Hamikdash is rebuilt and we have תרומה this will be very relevant, anyone taking a shower will need to go to the mikva.
The Mordechai applies the previous gezera in the gemara (if you take a shower after going to the mikva you are טמא) to hilchos nidda. The simple understanding of the gemara is that the chachamim made up a new טומאה and therefore it has no relevance to hilchos nidda. The Mordechai however learns that the pshat is that taking a shower cancels the tevila, and therefore a woman who goes to the mikva and then takes a shower is prohibited to her husband. We are machmir for this Mordechai לכתחילה. The poskim have different shiurim for how long she can't take a shower. One shiur given is until she is נוהג היתר with her husband, after that it is clear that the miva was matir and not the shower.
