Preheat the oven to 400F. Line a muffin pan with paper muffin liners and set aside.
In a large bowl, cream together eggs and both sugar. Add oil, pumpkin puree, and water, Mix until all ingredients are well incorporated.
In a separate bowl, sift together flour, baking powder and soda, cinnamon, nutmeg, and salt. Slowly add dry ingredients into wet ingredients and mix thoroughly. Pour half od the batter into a small bowl.
In a microwave safe bowl, melt 1/2 cup of semi-sweet chocolate chips and 1/2 cup of dark chocolate chips in 30 seconds intervals. Add cocoa powder to the chocolate mixture, then pour into the batter in a small bowl. Mix.
Fold the chocolate pumpkin batter into the rest of the batter and make a marble effect (do not mix).
Scoop batter into each muffin pan, filling about 3/4 of the way. Use the remaining chocolate chips to top off each muffin.
Bake for 20 minutes or until a toothpick comes out clean once inserted in the center. Allow to cool for 10 minutes on a wire rack.