In a small saucepan, bring 3 cups of water to a boil. Add the onions and turn off heat. Allow the onions to sit in the hot water for 1 minute. Drain and add onions to a small glass jar.
In a small mixing bowl, combine the water, cider vinegar, honey, and salt. Stir until salt and honey are dissolved. Pour mixture over the onions and sprinkle in the mustard seeds. Allow onions to sit in the vinegar solution for at least a few hours before serving. Keeps in the refrigerator for at least 2 weeks.