To make the soup base, combine the water, tomatoes, wine, leeks, carrots, onion, thyme, lemon zest, and saffron in a saucepan and bring to a boil. Lower the heat to a lively simmer and cook until reduced by about one third, about 45 minutes. Stir in ¼ cup olive oil, season the mixture lightly with salt, and continue to simmer until the liquid portion of the soup base is reduced to about 8 cups, about 20 minutes. Strain the soup base into a 3-quart saucepan and keep it warm over low heat. Discard the solids. (The soup base may be prepared up to 3 days in advance and refrigerated.)

If you have prepared the soup base in advance, bring it to a simmer in a medium saucepan. Adjust the heat to very low and keep warm. Heat ¼ cup olive oil in a large (about 8-quart), heavy pot over medium heat. Add the garlic, leeks, and onion and cook, stirring, until the onion is wilted but still crunchy, about 4 minutes. Add the calamari and cook, stirring, until they turn opaque, about 2 minutes. Pour in all but 1 cup of the hot soup base and bring to a boil. Stir in the scallops, fish fillets, and beans, if using. Adjust the heat to simmering and cook until the seafood is barely opaque at the center, about 5 minutes.

Meanwhile, add the mussels to the soup base remaining in the saucepan. Increase the heat to high, cover the saucepan, and steam over medium heat, shaking the pan occasionally, until the mussels open, about 3 minutes.

Stir the shrimp, parsley, and steamed mussels into the large pot of soup. Simmer until the shrimp is cooked through, about 1 minute. Check the seasoning, adding salt, if necessary, and pepper. Ladle into warm soup bowls, passing a basket of the bread of your choice separately.