For the brownies: Position a rack in the lower third of the oven and preheat to 325 degrees F. Butter a 9-by-13-inch baking pan and line with parchment paper, pressing the parchment into the corners and up the sides of the pan and leaving an overhang on 2 sides. Butter the parchment and dust lightly with flour.
Melt the 1 stick butter in a small saucepan or high-sided skillet over medium-low heat. Add the chopped chocolate and cook, stirring constantly, until mostly melted. Remove from the heat and continue stirring until the chocolate is completely melted. Transfer to a large heatproof bowl, let cool for 10 minutes and then whisk in the eggs, water and vanilla.
In another large bowl, combine the sugar, flour, cocoa powder, baking soda, baking powder and salt; whisk to combine. Transfer the dry ingredients to the melted chocolate then fold with a rubber spatula to combine. Pour the batter into the prepared baking pan. Set aside.
For the topping: Stir together the peanut butter, confectioners' sugar and melted butter in a medium bowl until smooth.
Spoon dollops of the peanut butter mixture on top of the brownie batter. Holding a butter knife vertically, swirl up and down and horizontally and vertically until the batter and topping are nicely swirled together. Sprinkle the chopped pretzels over the top.
Bake until a toothpick inserted into the center comes out with just a few crumbs, about 35 minutes.
Let the brownies cool in the pan on a wire rack for 30 minutes. Using the parchment "handles," lift the brownies out of the baking dish and transfer to a cutting board to cool completely before slicing into 12 bars.