Warm the water and kombu over medium heat: Combine the water and kombu in a 1-quart saucepan and set over medium heat.
Remove the kombu as the water comes to a boil: Remove the kombu from the water just before it comes to a full boil. (Boiling the kombu can make the broth bitter and a bit slimy.)
Add the bonito flakes and simmer: Add the bonito flakes, if using, and let the water come to a rapid simmer. Continue simmering for about 1 minute.
Steep the bonito flakes off the heat: Remove the pan from heat and let the bonito steep in the broth for an additional 5 minutes.
Strain the broth: Strain the bonito flakes from the both. Add additional water, pouring through the strained bonito, if needed to make 2 cups.
Use or store the broth: The broth can be used immediately, refrigerated for up to a week, or frozen for up to 3 months.