In a large bowl or in the bowl of a stand mixer, stir together the water, yeast, and sugar. Set the mixture aside until it's foamy and bubbling, about 5 minutes. Stir in the olive oil.
If you're using a stand mixer: Add the whole wheat flour, wheat germ, 1 1/4 cups bread flour, and salt to the bowl. Using the dough hook attachment, mix the ingredients at medium speed until a soft dough forms, then knead for 5 more minutes. Add more bread flour if the dough is sticky; it should adhere slightly to the bottom of the bowl but not to the sides.
If you're using your hands: With a wooden spoon, stir in the whole wheat flour, wheat germ, 1 1/4 cups bread flour, and salt until a soft dough forms. If needed, use your hands to work in the last of the flour. Sprinkle a dry work surface with flour. Turn out the dough and knead it until it's soft and pliable, about 10 minutes. Add more bread flour if the dough is too sticky to handle.
Oil a large bowl. With floured hands, place the dough in the bowl and turn it to coat it with the oil. Cover the bowl with a clean kitchen towel and set it in a warm spot to rise until doubled in bulk, about 1 hour and 15 minutes. You can use the dough immediately, cover and refrigerate it overnight, or freeze it for later use. (To freeze it, punch down the dough and wrap it tightly in plastic; thaw for 2 to 3 hours at room temperature or overnight in the refrigerator.)