Stir water, navy beans, carrots, celery, onion, fennel, garlic, tomato paste, bay leaves, salt, thyme and chili flakes in the slow cooker insert. Cook on low for 6 hours.
Stir olive oil into soup before serving.
Notes
Depending on the age of your beans, it may take them longer to cook. If they are still hard after six hours, put the lid back on and continue cooking for another hour.
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