Carbon dioxide is a natural byproduct of fermentation. Since fermentation is most active at warmer temperatures, the way to build up carbon dioxide (ie: carbonation) is to allow the water kefir to keep fermenting in a sealed bottle at room temperature.
Transfer your flavored water kefir into bottles using a funnel. Be sure to use bottles that are made to handle carbonation (both the glass and cap must be designed to seal and handle high pressure. They can be found at brewing supply stores like Preserved). Leave about an inch of head space from the top of each bottle. Let the bottles continue to ferment in a warm place, out of direct sunlight for anywhere from 12-72 hours, checking for carbonation (the “tssssss” sound) often; kefir ferments (and therefore carbonates) VERY quickly. Once carbonated, transfer to the refrigerator and consume within 1 month. Cold temperatures slow down, but do not stop fermentation. Even after refrigeration, always open bottles slowly over a sink in case of geyser-like carbonation.