Pulse fennel, onion, and garlic in a food processor or chop coarsely.
Heat oil in a large 5 or 6 quart heavy pot or dutch oven over medium-high heat until it shimmers, then stir in chopped vegetables, bay leaves, thyme, red-pepper flakes, 1 1/2 teaspoons salt, and 1/2 teaspoon black pepper.
Cook, covered, over medium heat, stirring once or twice, until vegetables begin to soften, about 4 minutes.
Add tomatoes with their juice, water, wine, and clam juice and boil, covered, 20 minutes. Stir in seafood and cook, uncovered, until fish is just cooked through and mussels open wide, 4 to 6 minutes (discard any that remain unopened after 6 minutes). Remove and discard bay leaves. Serve immediately with a crusty Italian bread.
Total time to serving is approximately 50 min. Yields 4 hearty servings.