Bring water to a boil in a large covered pot. Add beans, oil, garlic, red pepper flakes, fennel seeds, bay leaf, and parsley. Cook over medium heat, uncovered, for 1 hour, stirring occasionally. Add rice, pepper, and salt to taste. Reduce heat and simmer 1 hour more, stirring occasionally.

Slightly crush tomatoes with hands; stir tomatoes and juices into soup. Cook 30 minutes or until beans are soft. Salt to taste and sprinkle with fresh parsley to serve.