Heat oven to 350°F. Line 8-inch square pan with cooking parchment paper, leaving 1 to 2 inches paper hanging over sides.
Place cookie dough in bottom of pan; press to cover and form crust. Sprinkle 2/3 cup pecans evenly over dough; gently press in dough.
Bake on middle oven rack 10 minutes. Remove from oven to cooling rack; cool completely. Do not turn oven off!
Meanwhile, in 1-quart saucepan over medium heat, heat water and butter until butter is melted. Remove from heat. Stir in sugar and cocoa with whisk until combined. Cool 5 minutes. Stir in eggs with whisk.
Pour chocolate mixture over cooled crust. Sprinkle 1/2 cup chopped pecans over top.
Bake on middle oven rack 45 minutes. (If garnishing with finely chopped pecans, after 30 minutes of baking, quickly open oven and sprinkle pecans over top. Bake 15 minutes longer.) Remove from oven to cooling rack. Cool completely, about 1 hour.
To cut into bars, gently lift from pan using hanging paper. With sharp knife, cut into 4 rows by 4 rows to make 16 bars.