Add the flours, salt, and yeast to a deep bowl. Whisk to blend.
Pour in the water, and using a wooden spoon, stir until it forms a sticky dough.
Lightly flour a counter or large cutting board with some of the whole wheat pastry flour. Scrape the dough onto the surface, and lightly sprinkle some more flour on top. Knead the dough 3 to 5 minutes, adding more flour only as needed, until the dough forms a smooth, round ball.
Sprinkle some flour into a clean, deep bowl. Add the dough to the bowl, and cover tightly with plastic film. Let sit in a warm spot until doubled in volume, about 1½ hours. Proceed with desired pizza recipe.