Preheat oven to 350 degrees F (175 degrees C). Grease 9 muffin cups or line with paper liners.
Stir water and flax seed meal together in a bowl; set aside until "flax egg" is thickened, about 10 minutes.
Whisk gluten-free all-purpose flour, pecans, coconut flour, baking soda, baking powder, and salt together in a large bowl. Add flax egg, maple syrup, coconut oil, and vanilla extract to flour mixture and mix well until batter is smooth. Scoop batter into the prepared muffin cups.
Bake in the preheated oven until muffin tops are starting to brown, about 17 minutes. Cool muffins in the tin for a few minutes before removing.