Position a rack in the center of the oven and heat the oven to 375°F Lightly butter a 9-inch square metal or ceramic baking pan.
In a small bowl, combine the flour, brown sugar, cinnamon, and 1/8 teaspoons of the salt. With your fingers, work the butter into the flour mixture until the mixture readily clumps together when pressed. Mix in the pecans.
In a large bowl, toss the blueberries and peaches. In a small bowl, combine the granulated sugar with the cornstarch, nutmeg, and the remaining 1/8 teaspoons salt and toss this mixture with the fruit.
Spread the fruit into the prepared baking pan. Pressing the streusel into small lumps, sprinkle it over the fruit. Bake until the fruit is bubbling in the center and the topping is crisp and well browned, 45 to 50 minutes. Cool slightly and serve warm.