Bring 10 cups water and navy beans to a boil in a large pot; cook at a boil for 2 minutes. Stir bacon, onion, brown sugar, molasses, and salt into water.
Carefully pour mixture into a slow cooker.
Cook on High, stirring occasionally, for 4 hours.
Stir 3 cups water into mixture. Continue cooking until beans are tender, about 2 hours 15 minutes more.