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 160ºF 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.
Let the broth cool to room temperature before storing in an airtight container in the refrigerator. Use within 1 week or freeze for up to 1 month.