Preheat oven to 400 degrees F (200 degrees C). Grease a 9x13-inch baking dish with about 1 teaspoon olive oil.
Place trout in the prepared baking dish and coat with remaining olive oil. Season the inside and outside of fish with dill, thyme, and salt. Stuff each fish with onion slices; grind pepper over the top. Place 1 lemon slice on each fish.
Bake in the preheated oven for 10 minutes; add water to dish. Continue baking until fish flake easily with a fork, about 10 minutes more.
