In a large pot over medium heat, cook the diced bacon until crisp, about 5–7 minutes. Transfer bacon to a plate with a slotted spoon, leaving the drippings in the pot.
Add butter to the pot. Stir in the onion and celery and cook until softened, about 5 minutes. Add the garlic and cook for 1 minute until fragrant.
Sprinkle the flour over the vegetables and stir constantly for 2 minutes to form a roux (this thickens the chowder).
Slowly pour in the clam juice and water, stirring well to prevent lumps. Bring to a gentle boil.
Add the diced potatoes. Reduce heat and simmer until potatoes are fork-tender, about 15 minutes.
Stir in the clams (with their juice) and the half-and-half. Warm over low heat for about 5 minutes. Do not boil after adding dairy.
Season with salt, pepper, and optional cayenne and thyme. Taste and adjust seasoning.
Optional thicker chowder: Mix cornstarch with cold water to make a slurry. Stir it into the simmering chowder and cook 1–2 minutes until slightly thickened.
Stir in most of the bacon, reserving a little for garnish. Serve hot with parsley and oyster crackers or crusty bread.