Boil diced potatoes and shredded carrot in just enough water to cover. When fork-tender, do not drain, just coarsely mash and set aside.
Meanwhile, melt butter in large heavy pot.
Add onion and cook until soft.
Add flour. Stir to remove any lumps.
Slowly add milk. Stir until smooth.
Add diced bell pepper. Heat slowly to scalding, stirring regularly to prevent scorching. Do not boil.
Add cooked potatoes and carrots.
Add clams with juice and heat through. (The clams are already cooked and only need to be heated through, so they don't get tough.)
Season with salt and pepper to taste.