In a liquid measuring cup, pour in the warm water. Mix in the brown sugar and yeast and let the mixture sit for 5 minutes.
In a mixing bowl, whisk together the flour and salt. Add the yeast mixture and mix until it forms a dough. Knead for 10 minutes. Cover the dough and let it rest for 2 hours.
Place the dough on a floured surface. Divide it into 8 even pieces, using a kitchen scale if you can, and shape each piece into a ball. Use your thumb to press a hole through each dough ball, then gently stretch it until it forms a bagel shape.
Place the bagels on a baking tray and let them rest for 30 minutes. Spread the baking soda on a baking pan and bake for 30 minutes, which will create a darker brown crust for the pretzels (optional).
Preheat the oven to 425º F.
Mix the baking soda with 6 cups of filtered water. Bring 8 cups of water to a boil over medium-high heat in a large pot.
Boil each bagel for 2 minutes on each side, flipping with tongs or a slotted spoon. Place them into the baking soda bath for 15 seconds on each side, then place back onto the baking sheet. Sprinkle with pretzel salt.
Bake the pretzel bagels for 20-25 minutes, or until they are brown on the outside. Remove the bagels from the oven and let them cool before serving.