Preheat oven to 350°F. Line an 8x8 baking pan with foil or parchment paper. Lightly grease the foil/parchment.
In a medium bowl combine cocoa powder, powdered sugar, flour, salt, and chocolate chips. Set aside.
Melt butter in a large microwave safe bowl (the butter should still be very warm). Immediately add granulated sugar and whisk until combined. Allow the mixture to sit at room temp for 5 minutes. After 5 minutes, whisk the mixture vigorously for about 30 seconds. Add eggs, water, and vanilla extract. Whisk until well combined.
Add the dry ingredients to the wet ingredients and use a rubber spatula or wooden spoon to stir the mixture until it is glossy and well combined.
Scoop the batter into the prepared pan and smooth the top. Bake for 27-32 minutes. The brownies should be underbaked just slightly. If you insert a toothpick into the center it should come out with moist fudgy crumbs, but no raw batter. Place the pan on a wire rack to cool. Immediately begin the pecan topping.
Pecan topping:
Melt butter in a medium sized saucepan. Add cream, brown sugar, syrup, and salt to the melted butter and whisk to combine. Bring to a simmer over medium-low heat and simmer for 5 minutes, whisking frequently. Remove from the heat and stir in vanilla and pecans. Set aside for 15 minutes to cool slightly. It should thicken up just a bit but still be pourable.
Carefully pour the pecan topping over the brownies and gently spread it into an even layer. Sprinkle with flaky sea salt, if desired. Allow to cool completely before cutting and serving. The topping will firm up once chilled.
Notes
* To toast pecans: place pecans in a dry skillet over medium heat. Cook, stirring occasionally, until fragrant and lightly toasted. Watch them carefully so they don't burn. STORAGE: Store at cool room temperature or the refrigerator for 3 days. Brownies can be frozen for up to 3 months. SERVING: Enjoy the brownies warm, room temperature, or chilled. The topping will firm up when chilled.SHORTCUT OPTION: Feel free to use a boxed brownie mix in place of the homemade brownie portion of this recipe. Bake the brownies fully and then add the pecan pie topping. Be sure your boxed brownies are baked in an 8x8 pan so that you have enough topping.