Heat oil in a large pot over medium heat. Add fennel and shallots and cook until soft and translucent, 6 minutes. Add garlic, oregano, and red pepper flakes and season with salt and pepper. Cook until fragrant, 1 minute more.
Add wine and let boil until reduced by half, 3 to 5 minutes, scraping up browned bits with a wooden spoon. Add tomatoes, clam juice, water, bay leaves, and orange zest (if using). Stir to combine, bring to a low simmer, and cook, stirring occasionally, for 20 minutes.
Remove bay leaves and orange zest. Add clams to simmering broth, cover, and cook for 5 minutes. Uncover, add mussels in an even layer, then shrimp, then halibut. Do not stir. Cover again and cook for 5 more minutes, or until all clams and mussels are opened and shrimp and fish is cooked through and opaque. Discard any unopened mussels and clams. Season with salt and pepper to taste.