Bring water and brown rice to a boil in a saucepan. Reduce heat to medium-low, cover, and simmer until rice is tender and liquid has been absorbed, about 40 minutes; transfer cooked rice into a large mixing bowl.

Preheat the oven to 350 degrees F (175 degrees C).

Meanwhile, heat a large skillet over medium-high heat. Break ground beef into small pieces and place in the skillet. Add onion, mushrooms, and garlic; cook and stir until the beef is completely browned, 7 to 10 minutes. Mix beef mixture into brown rice.

Stir tomato sauce, diced tomatoes, tomato paste, and Italian seasoning into the rice mixture; season with salt and pepper.

Arrange bell peppers in a baking dish; spoon a generous amount of filling into each bell pepper.

Bake in the preheated oven until peppers are tender, about 1 hour. Sprinkle Parmesan cheese over the stuffed peppers to serve.