Pour off 3 1/2 cups of the soaking liquid and reserve. Drain and discard remaining soaking liquid. In a 3-quart saucepan, sauté bacon until it begins to crisp, about 5 minutes.
Add onions, bell pepper, cumin, and ½ tsp. salt. Continue to cook about 5 minutes longer, until vegetables are softened.
Stir in garlic and oregano and cook until fragrant, about 30 seconds. Add water, beans, bay leaves, and red pepper flakes. Bring to a boil.
Pour into a large crock pot and cook on HIGH for 3 to 4 hours or LOW 7 to 8 hours (see notes).
Remove and discard bay leaves. Add cilantro and lime juice and season to taste with salt and pepper.
Slow cooker times may vary. The first time you make the beans, please check them after 3 or 4 hours on HIGH and continue cooking longer if necessary. If the beans have any crunch to them at all, please cook them longer.To soak black beans: Place 4 quarts water in a large bowl and add beans. Soak at least 8 hours or overnight.Adapted from America's Test Kitchen Healthy Cookbook.