Combine the flax seed and water and set aside to thicken for a couple minutes.
In a large bowl, combine the sweet potato (or pumpkin) puree with the almond milk and whisk well. Slowly pour in the butter while whisking vigorously. Add the brown sugar and the flax seed mixture and whisk until combined.
In another bowl, combine the flours and the rest of the dry ingredients. Mix until combined. Add the dry ingredients to the wet and stir until just combined - it should be a slightly thick batter.
Heat your waffle iron to medium. Grease the iron with non-stick stray and add an appropriate amount of batter, spreading it around as necessary (this may take a time or two to get the hang of).
Cook until the waffle is no longer steaming profusely. This took about 6 minutes per waffle in my belgian waffle maker, but may take more or less time depending on the shape of waffles you make.
Serve immediately with some extra butter and maple syrup on the side. Enjoy!