Preheat an oven to 325 degrees F (165 degrees C). Combine the flour, baking soda, and salt in a small bowl; set aside. Grease and flour a 9x9-inch baking dish.
Combine the sugar, water, and butter in a saucepan. Cook and stir over medium heat until the butter has melted and the sugar has dissolved. Remove from the heat and stir in one bag of chocolate chips and the vanilla extract until the chocolate has melted. Pour the mixture into a mixing bowl, and beat in the eggs one at a time until smooth. Fold in the flour mixture until incorporated, then fold in the remaining bag of chocolate chips along with the walnuts. Pour into prepared pan.
Bake in the preheated oven until the top is dry and the edges have started to pull away from the sides of the pan, 45 to 55 minutes. Cool completely before cutting into squares to serve.