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 appear around the sides of the pan, 9 to 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. Reserve the bonito flakes for another use.
Store in an airtight container in the refrigerator. Use within 1 week or freeze for up to a month.