In a saucepan, add the clams and water. Bring to a boil and cook for 5 minutes, or until the clams are cooked through. Turn off the heat, drain the clams, and remove the shells, reserving the cooking water. Set the clams aside.
Dry the saucepan with paper towels and heat it over medium heat. Add the bacon and cook until crispy. Remove the bacon from the saucepan and place it on paper towels to drain excess oil.
Add the onion to the saucepan and stir-fry until aromatic and nicely browned. Then, stir in the all-purpose flour and cook until well blended. Add 2 cups of the clam-boiled water, stir, and bring the soup to a boil.
Next, add the potatoes, garlic salt, dried thyme, and ground black pepper. Stir constantly to avoid the potatoes sticking to the bottom. Bring the soup to a boil, then lower the heat. Cover and simmer for 15 to 20 minutes, stirring occasionally.
Once the potatoes are tender and soft, stir in the milk and add the clams. Heat through.
Serve immediately, topped with crispy bacon and parsley.