Put the kombu in a 4-quart saucepan, cover with the water and soak for 30 minutes.
Set the saucepan over medium heat until the water reaches 150 to 160 degrees F and small bubbles begin to appear around the sides of the pan (~ 10 minutes)
Remove the kombu from the pan
Increase the heat to high and bring to a boil (~ 5 to 6 minutes)
Reduce the heat to low and add the bonito flakes. Simmer gently, stirring frequently, for 10 minutes
Strain the liquid through a fine mesh strainer lined with muslin or several layers of cheesecloth
Store in an airtight container in the refrigerator. Use within a week or freeze for up to a month