Preheat oven to 330 degrees F (166 degrees C). Grease 24 muffin cups or line with paper liners.

Mix whole wheat flour, all-purpose flour, pumpkin pie spice, baking soda, and salt together in a large bowl. Whisk pumpkin pie filling, sugar, oil, water, and eggs together in a separate bowl until just mixed. Stir flour mixture, about 1/4 cup at a time, into pumpkin mixture until batter is just combined. Fill muffin cups with batter just below the brims.

Bake in the preheated oven until a toothpick inserted in the center of a muffin comes out clean, about 30 minutes. Cool muffins on a wire rack.