Combine water and bonito; let stand 2 minutes. Strain the liquid through a fine sieve into a bowl; discard solids. Bring the liquid to a boil in a large saucepan. Add yellow and red miso and soy sauce; stir well with a whisk until smooth. Divide the enoki mushrooms and tofu evenly among 6 soup bowls, and ladle 1 cup soup into each bowl.
I found this soup to be a little boring. My bonito might have been part of the problem. I had my bonito flakes in the pantry for a while but they were individually packaged so I thought they were still ok but maybe they had lost some of their flavor. I substituted instant miso since that's all my grocery store had. I also added a few slices of shiitake mushrooms and I liked the extra texture. If I made this again I would add some green onions.