Decantar literally means "to decant", a process of allowing sediment in a liquid, like wine, to settle. It's a sophisticated and uncommon word to find in a pop song.
Shakira uses it in a beautiful metaphor for healing. She sings that life itself will "decantar la sal que sobra del mar" (settle the excess salt from the sea), poetically suggesting that life will naturally filter out the pain and sorrow, leaving peace behind.
This is such a sweet and personal love song from Shakira! She tells the story of meeting someone special on a January day: "Te conocí un día de enero / Con la luna en mi nariz" (I met you on a January day / With the moon on my nose). From the start, she sees he's been hurt in the past, finding "varios rasguños" (several scratches) on him from his life before her. But she promises to fix it, telling him her "loco amor / Es tu mejor doctor" (crazy love / Is your best doctor).
Shakira fills the song with little details that seem to point to a real person. She mentions he feels like an "extranjero / Hasta en tu propio país" (a foreigner / Even in your own country) and that he uses specific Argentine slang, saying "¿qué decís?" instead of the "¿cómo dices?" she uses. He even cries when he hears a bandoneón, an instrument central to tango music. The whole song is her promise to heal his aching heart and help him see "el sol brillar" (the sun shine) again, because as she says, "Tú más que nadie mereces ser feliz" (You more than anyone deserve to be happy).