Gather all ingredients.

Heat 3 tablespoons olive oil in a large skillet over medium heat; cook and stir sea scallops, shrimp, and calamari rings in the hot oil until scallops and calamari are opaque and shrimp are pink, about 5 minutes.

Bring a separate pot of water to a boil and add mussels and littleneck clams to the boiling water; cook until shells have opened, about 3 minutes.

Remove shellfish and rinse with hot water.

Pour crushed tomatoes, water, 2 cans chopped clams, 1/4 cup olive oil, onion, red pepper flakes, garlic, oregano, parsley, and salt into a large pot and bring to a boil.

Stir cooked scallops, shrimp, calamari, mussels in shells, and littleneck clams in shells into tomato mixture. Reduce heat to low and simmer for 1 hour.

About 10 minutes before serving, bring a large pot of lightly salted water to a boil; cook the linguine at a boil until tender yet firm to the bite, about 10 minutes; drain and rinse pasta in hot water to prevent sticking.