Preheat your oven to 425°F. Line two large baking sheets with parchment paper and coat with cooking spray.
In a shallow bowl, whisk together almond flour, 1/2 cup Parmesan, Italian seasoning, and sea salt.
In another shallow bowl, whisk the eggs with 2 tablespoons of water, then season with a pinch of salt and black pepper.
Dip each eggplant slice into the egg wash, allowing excess to drip off, then sprinkle the flour mixture evenly over both sides. Place coated slices on the prepared baking sheets.
Lightly spray the tops of the eggplant slices with cooking spray. Bake for 30 minutes, flipping slices halfway through, until golden and crisp.
Spread 1 cup of marinara sauce evenly across the bottom of a 9x11-inch baking dish.
Add a layer of baked eggplant slices, trimming as needed to fit. Follow with 1 cup of marinara, 1 cup of mozzarella, 1/4 cup Parmesan, and 1/4 cup basil.
Repeat the layers, finishing with a final layer of eggplant, marinara, mozzarella, Parmesan, and basil.
Bake uncovered for 15-20 minutes, until cheese is bubbly and golden. Enjoy warm!