Bring brown rice and water to a boil in a saucepan. Reduce heat to medium-low, place a cover on the saucepan, and simmer until the rice is tender, about 40 minutes; transfer to a large mixing bowl.
Preheat oven to 350 degrees F (175 degrees C).
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 and season filling with salt and black pepper.
Arrange bell peppers in a baking dish. Spoon filling into bell peppers.
Bake in preheated oven until the peppers are tender, about 1 hour. Sprinkle Parmesan cheese over the stuffed peppers to serve.
