In a large saucepan over medium high heat, combine the butter, celery and onion. Saute for about 3 minutes, add the flour and stir well to make a dry roux. Add the reserved clam juice to make a paste, then slowly add enough cold water to reach the desired thickness.
Add the potatoes, milk, thyme and salt and pepper. Reduce heat to low and allow soup to simmer for about 20 minutes, or until the potatoes are tender. Add the clams and allow to heat through.