Grease a nonstick skillet with cooking spray and heat over medium heat. Add onion; cook and stir until slightly softened, about 2 minutes. Add artichoke hearts and cook until heated through, 1 to 2 minutes. Stir in spinach and tomatoes; cook until spinach is wilted, about 5 minutes. Transfer to a bowl.
Whisk eggs, water, and pepper together in a bowl.
Wipe out skillet; spray with cooking spray. Heat over medium heat. Pour in egg mixture; cook until mostly set, about 3 minutes. Gently push cooked edges into the center; tilt skillet so uncooked eggs flow underneath. Cook until set, 2 to 4 minutes. Spoon spinach mixture over 1 side of the omelet. Fold in half and serve.