Place carrots in a 32 ounce spring-top glass jar. Bring the water, sugar, apple cider vinegar, onion powder, mustard seeds, salt, and red pepper flakes to a boil in a non-reactive saucepan. Boil for 4 minutes.
Slowly pour the hot pickling liquid over the carrots, filling the jar to the top. Place the chilies in the jar. Allow the carrots to cool before sealing. Refrigerate for 2 days or up to 1 week.