In a large pot, cover beans with cold water, and soak overnight. (Or do a quick soak in a pressure cooker by covering with 3 inches of water, sealing, and cooking at high pressure for three minutes before cooling.) Drain and rinse well. Return beans to the pot, cover again with cold water, and bring to a boil. Lower heat and simmer for 60-90 minutes, until tender.
While beans are cooking, preheat oven to 350°F. Heat oil in a Dutch oven or large saute pan over medium heat on the stove. Saute the onion and garlic for 5 minutes, until translucent and fragrant. Add the tomatoes, water, dill, oregano, salt and pepper, and bring to a simmer.
When beans are tender, drain, reserving 2 cups of liquid. Stir them into the tomato mixture, coating well. (Add some of the bean liquid if there’s not enough sauce.) Transfer to the oven, uncovered. Bake for 30-40 minutes, until beans are tender, adding more of the cooking liquid, if needed.