Cut each calamansi lime in half, and then squeeze the juice through a sieve and into a small container. Set aside the calamansi rinds. Discard the seeds in the sieve and save the calamansi juice for another use.
Place the reserved rinds, sugar, and water into a saucepan over high heat and bring to a boil while stirring frequently. Reduce the heat to low, and simmer for 10 minutes, stirring until the sugar dissolves. Remove from the heat, and then cover the pot and allow the syrup to cool completely to room temperature.
Pour the syrup through a fine mesh sieve set over a large bowl. Press down on the rinds in the sieve to extract as much liquid as possible. Discard the rinds. Store calamansi syrup in a lidded container and refrigerate for up to a month.