Preheat the oven to 425°F. Coat a rimmed baking sheet with cooking spray. Trim and peel the beets, and cut them into bite-size wedges.
Toss the beets with the olive oil, salt, and pepper on the prepared baking sheet. Bake for 30 to 35 minutes, turning after 15 minutes, until the tip of a paring knife can easily pierce them. Remove the beets from the oven and let cool.
Make the dressing: Whisk together the vinegar, mustard, and honey in a medium bowl. Gradually whisk in the oil and stir until thickened. Season with salt and pepper to taste.
Combine the arugula, cooled beets, watermelon, onion, and pepitas in a serving bowl. Drizzle with the dressing and sprinkle with the goat cheese. Toss gently to combine. Serve immediately.