In the bowl of a stand mixer fitted with the dough hook, combine the whole wheat flour, rye flour, and water. Stir to mix and let sit for 20 to 30 minutes to hydrate. Add the sponge with the yeast, honey, and salt. Mix on low speed until the ingredients are fully incorporated, 2 to 3 minutes. Increase the speed to medium for 3 to 4 more minutes, until the dough is smooth and pulls away from the sides of the bowl. If you don’t have a stand mixer, combine the ingredients in a large bowl using a wooden spoon to mix and then knead the dough on a lightly floured surface until it is smooth, elastic, and cohesive.
Place the dough in a large lightly-oiled bowl. Cover with plastic wrap and let rise for 60 to 90 minutes.
Divide the dough into two equal pieces and shape into rounds. Cover and let rest 30 minutes.
Pat each dough piece into a disk and roll it into a loaf shape. Place each in a well-oiled 4-by-8-inch loaf pan. Cover the loaves with a clean plastic bag or tea towel and let rise, or proof, for 2 to 3 hours at room temperature.
Preheat the oven to 450°F.
Score each loaf down the middle with a sharp knife and bake for 25 minutes. Reduce the temperature to 400°F and bake for another 15 to 20 minutes. The bread will be a rich brown color.
Let the loaves partially cool in the pans, then turn them out onto a wire rack to cool completely.