Preheat oven to 350 degrees F (175 degrees C). Grease a baking sheet or line with parchment paper.

Mix water and ground flax seed together in a bowl, creating a "flaxegg"; set aside until thickened, about 5 minutes.

Combine whole wheat flour, oats, baking powder, baking soda, salt, nutmeg, and cinnamon together in a bowl. Beat raw sugar, coconut sugar, and coconut oil together in a separate bowl using an electric mixer until smooth; add pumpkin puree, flaxegg, and vanilla extract and mix well.

Pour pumpkin mixture into flour mixture and stir just until dough is combined; fold in chocolate chips and pecans. Scoop dough onto the prepared baking sheet using a small ice cream scoop.

Bake in the preheated oven until lightly browned around the edges, about 10 minutes. Cool cookies on the baking sheet for 5 minutes before transferring to a wire rack to cool completely.