Preheat oven to 375°. Grease or line baking sheets.
Whisk together flour, cocoa, baking soda, and salt. Set aside.
Beat sugar, brown sugar, butter, and peanut butter until light and fluffy. Add vanilla, egg, and water, and mix well.
Gradually add dry ingredients, mixing well. Stir in peanut butter cups.
Drop dough by tablespoonfuls onto prepared pans. Flatten each cookie to about 1/2-inch thick.
Bake 7-9 minutes, or until cookies are set. Cool cookies on pan on wire rack.
Makes about 3 dozen cookies.