In a food processor, combine flour, cheese, and butter. Pulse until it’s a crumbly texture, but well combined. Add water and process until a dough forms. Divide dough into two balls and chill for 15 minutes in the refrigerator, until firm.
Roll one ball in between two sheets of wax paper. Roll to about 1/8 to 1/4 inch thick (the thinner the dough the crispier the cracker. Pull top sheet of wax paper off and cut dough into 1 inch squares using a pizza cutter (can use a knife). Pick up dough using wax paper and invert onto a parchment paper lined baking sheet. Carefully peel off the wax paper. Sprinkle lightly with sea salt.
Poke holes in center of each cracker with a toothpick. Bake for 10-15 minutes until edges are lightly brown. Remove from oven and recut the crackers, just trace the line you made before. Allow to cool completely before breaking apart. Repeat with second dough ball.
You can store crackers in an air tight container in refrigerator for one week.