Warm the oil in a large saucepan or stockpot over medium-high heat. Add the onion, carrots, celery, and jalapeño and cook until tender but not brown, about 5 minutes. Add the broth, wine, water, potatoes, thyme, and salt. Increase heat to high and bring to a boil.
Reduce heat to medium and simmer, partially covered, 10 minutes. Add the tomatoes and return to boiling. Stir in scallops, shrimp, and baby clams (with the juice). Cover and cook over medium-high heat, just until the scallops and shrimp turn opaque, about 7 minutes.