Preheat the oven to 275 degrees F (135 degrees C). Line a baking sheet with parchment paper.
Whisk brown sugar, water, salt, molasses, cumin, cinnamon, ginger, cayenne pepper, and nutmeg together in a medium mixing bowl. Add pumpkin seeds and toss until evenly coated. Transfer to the prepared baking sheet.
Bake until crispy, stirring halfway through, 35 to 40 minutes. Remove from the oven, stir, then carefully slide or lift the parchment paper off the baking sheet and set on the counter to cool completely. Break up any clumps with your hands and serve.