Preheat oven to 325°F. Prepare muffin tins by greasing or using a muffin tin liner.
Sift together dry ingredients (flour, baking soda, salt, cinnamon, nutmeg and sugar).
In a separate bowl, beat together wet ingredients (canola oil, applesauce, eggs, water, pumpkin and vanilla).
Add dry ingredients to wet ingredients. Mix well but do not over-manipulate. Stir in chocolate chips. Spoon into prepared muffin tins.
Bake for 25 minutes. Pop out muffins halfway after removing from oven to prevent overbaking.