"This Dicastery is able to respond that the removing of Holy Water from the fonts during the season of Lent is not permitted, in particular, for two reasons:
1. The liturgical legislation in force does not foresee this innovation, which in addition to being 'praeter legem' is contrary to a balanced understanding of the season of Lent, which though truly being a season of penance, is also a season rich in the symbolism of water and baptism, constantly evoked in liturgical texts.
2. The encouragement of the Church that the faithful avail themselves frequently of the sacraments is to be understood to apply also to the season of Lent. The 'fast' and 'abstinence' which the faithful embrace in this season does not extend to abstaining from the sacraments or sacramentals of the Church. "The practice of the Church has been to empty the Holy Water fonts on the days of the Sacred Triduum in preparation of the blessing of the water at the Easter Vigil, and it corresponds to those days on which the Eucharist is not celebrated (i.e., Good Friday and Holy Saturday)."
I found this linked up on Zenit here (at the bottom of the article), but the same statement is easily available from many other sites including Fr. Z.