For the brownies: Position a rack in the lower third of the oven; preheat the oven to 325 degrees F. Butter a 9-by-13-inch baking dish 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 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 totally melted. Transfer to a bowl, let cool for 10 minutes and then whisk in the eggs, water and vanilla.
In a separate large bowl, add the sugar, flour, cocoa powder, baking soda, baking powder and salt. Whisk to blend. Add the dry ingredients to the melted chocolate mixture; with a rubber spatula, fold to combine. Pour the batter into the prepared baking dish. Set aside.
For the topping: Mix the peanut butter, confectioners' sugar and melted butter together 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 chocolate batter and peanut butter topping are nicely swirled together. Sprinkle the chopped pretzels over the top.
Bake for 35 minutes, or until a toothpick inserted into the center comes out with just a few crumbs.
Let the brownies cool in the pan on a baking 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.