The nun who ran the Novus Ordo parish I once went to used to fill the holy water fonts with sand during Lent. She said it had something to do with the desert, but I never understood it. The parish was a in a farming community and the people didn't like it and complained until she eventually stopped doing it.
In the Catholic Church, the holy water fonts are never emptied (though they may, through inattention, by dry on occasion). Holy water is needed most during Lent.