Toast the pistachios in a medium skillet over medium-low heat, shaking the pan occasionally, until they are fragrant and lightly toasted, 5-7 minutes. Transfer to a cutting board and let cool, then coarsely chop.
Halve two naval oranges and squeeze enough juice to yield 1/2 cup; set aside. Using a sharp paring knife, cut the peel and pith from the remaining oranges, then slice the fruit into thick rounds.
Whisk together the orange juice, vinegar, honey, 1/4 teaspoon salt, and a generous grinding of pepper in a bowl. Whisk in the oil.
Arranges the oranges, beets, fennel, and onion on a serving platter.
Whisk the dressing again to blend, and spoon over the salad. Top with the pistachios, mint, and fennel fronds. Season with flaky sea salt and pepper.