Prep the pan and bread: Grease a 9x13-inch baking dish.
Spread the cubed bread on a sheet pan and toast in a 325°F (165°C) oven for 10–12 minutes to dry it out slightly. This helps the custard soak in without getting soggy.
Make the caramel: In a medium saucepan, combine sugar and water. Cook over medium heat without stirring until the mixture turns deep amber, 7–10 minutes.
Off the heat, whisk in butter, then slowly whisk in warm cream. Add salt. Set aside to cool slightly.
Whisk the custard: In a large bowl, whisk eggs, milk, cream, granulated sugar, brown sugar, vanilla, cinnamon, nutmeg, and salt until smooth.
Assemble: Add toasted bread and chopped pecans to the baking dish.
Pour about half of the caramel sauce over the bread and toss gently to coat. Pour the custard over everything, pressing down lightly so all pieces soak up the mixture. Drizzle melted butter over the top.
Rest: Let the mixture sit for 15–20 minutes so the bread absorbs the custard.
Meanwhile, heat the oven to 350°F (175°C).
Bake: Cover loosely with foil and bake for 25 minutes. Remove foil and bake another 20–25 minutes, until the top is golden and the center is just set. A knife inserted in the center should come out mostly clean with a little moisture.
Finish and serve: Warm the remaining caramel if needed.
Let the bread pudding rest for 10 minutes, then serve warm with extra caramel drizzled on top. Add ice cream or whipped cream if you like.