In a glass measuring cup, combine lime zest and juice, 2 tbsp. agave, and 6 tbsp. water. Taste and add more agave if you like. Divide mixture among 8 (1/3 cup) popsicle molds*. Cover and freeze until partially solid, 1 to 1 1/2 hours.
Meanwhile, in a food processor, whirl cantaloupe and 2 tbsp. agave until smooth. Transfer to a glass measuring cup and chill in refrigerator. Rinse food processor bowl, then whirl watermelon and 3 tbsp. agave until smooth. Pour mixture into another glass measuring cup and chill.
Stir cantaloupe purée and divide among popsicle molds. Freeze until partially solid, 1 hour. Stir watermelon mixture, then spoon an equal amount into each popsicle mold. Press popsicle sticks through all the layers. Cover and freeze pops until solid, 2 to 3 hours more.
To remove popsicles from molds, either let sit at room temperature 5 minutes or run molds under warm water 10 to 15 seconds. (If molds are metal, cut the time to just a second; otherwise the pops melt.)
*We used Onyx 1 8/8 stainless steel popsicle molds ($32; amazon.com).
Make ahead: Up to 2 weeks, frozen.