Pick through the black beans, making sure there are no twigs, stones, or shriveled beans in the mix. Give them a quick rinse in a colander, then pour the beans into a medium (5-quart) dutch oven or heavy-bottomed soup pot. Cover the beans with water by two inches, then leave to soak for 8 to 12 hours.
After the beans have soaked, they will have expanded considerably. Add enough extra water to cover the now-larger beans by one inch, then add the onion, garlic, thyme, and bay leaves.
Heat the dutch oven over medium-high heat until the beans come to a boil, then let boil for five minutes.
Turn the heat down to low and simmer for about 45 minutes, then add the salt and continue to simmer until the beans are tender but not falling apart, about another 45 minutes.