I have seen some churches empty the holy water fonts during the entire Lenten season…...does the Church tell us to do this? What is the meaning behind this practice?

In recent years, some parishes have taken the holy water out of the holy water fonts during Lent. I have even seen fonts filled with sand in some cases. The idea, they say, is to convey the thought that Lent is a time of spiritual dryness--a “desert” experience--that precedes Easter, in which we refrain from using the sacramental of holy water. Despite its popularity in some places, this practice is not permitted.
 
It has been the Church’s practice to empty the holy water fonts during the Sacred Triduum (Holy Thursday, Good Friday, Holy Saturday), but for a different reason. It is not permitted to have them empty through the whole season of Lent.
 
The Congregation for Divine Worship in Rome provides us with the following guidelines: 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 apart from the law, 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 sacrament 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 sacramental of the Church.

 
The practice of the Church has been to empty the Holy Water fonts on 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). So keep on using that holy water during Lent, folks.