Combine the nuts, garlic, spinach, and arugula in a food processor and puree. Next add the lemon zest, juice, oil, salt, pepper, and red pepper flakes (optional); puree until smooth. Divide pesto into two bowls and set aside or refrigerate.
Place fish in a baking dish. Using pesto from one bowl, gently brush pesto on fish, flip to coat other side. Cover and place in refrigerator to marinade for 30 minutes.
Preheat the oven to 400°F.
Place the marinated fish on a nonstick or a parchment paper-lined baking sheet. Bake for 10 minutes per inch of thickness, about 15 to 25 minutes, or until done.
Top fish with fresh pesto from second bowl. Serve.