In a 2-qt. microwave-safe dish, combine carrots and 2 tablespoons water. Cover and microwave on high for 2 minutes; stir. Cover and cook 2 minutes longer or until tender. Add broccoli. Cover and microwave for 2 minutes; stir. Cover and cook 1 to 1-1/2 minutes longer or until vegetables are tender. Stir in milk.
In a small bowl, combine the flour, bouillon, salt and pepper; stir in remaining water until smooth. Stir into broccoli mixture. Cover and microwave on high for 6-7 minutes or until mixture is boiling and thickened, stirring every minute. Stir in cheese until melted.