Preheat oven to 325 degrees. Pat chuck roast dry and season with salt and freshly ground black pepper all over.
In a Dutch oven over high heat, heat oil until shimmering. Brown beef on all sides until a deep brown crust develops, about 7 to 10 minutes. Transfer beef to cutting board or platter.
To the Dutch oven, add carrots, onions, and potatoes and cook stirring occasionally, until vegetables begin to brown, about 5 minutes. Add garlic and cook until fragrant, about 30 seconds. Stir in red wine, deglaze the pan by scraping up brown bits.
Add beef broth, tomato paste, thyme, bay leaf, 1 teaspoon salt and 1/2 teaspoon freshly ground black pepper and bring to a simmer. Return beef to pot. Cover and bake until meat is tender, about 4 hours. Remove the beef and vegetables (discard bay leaf) and keep warm while making the gravy.
To make the gravy, pour drippings into a bowl. Allow the fat to rise to the top. Skim off fat and reserve 1/4 cup. In a large saucepan over low heat, add reserved fat. Whisk in flour and stir until the mixture is bubbly. Set aside to cool.
Measure remaining meat juices and add water until it reaches 2 cups of liquid. Add mixture to saucepan, return to medium-high heat and bring to a boil, stirring constantly. Boil until mixture thickens, about 1 minute. Season to taste with salt and pepper. Serve pot roast with vegetables and top with gravy.